[Bug]: Process breaks when running more than one instance of a program

[Sollace]

Describe the bug

If you open two instances of the same program (so using the same bottle) and then close the most recent one to open, the remaining instance stops responding and becomes unrecoverable.

This becomes most noticeable when you have a file association set up to open files with the bottle program, and so opening more than one file at a time spawns multiple instances.

If you close the first one opened, then the most recent one opened continues functioning.

The behaviour gets harder to predict with more than two instances but I suspect it follows the same rules.

To Reproduce

1. Install the bottles flatpak. I am running 51.21
2. Create a new bottle with the "Application" configuration and soda-9.0.1 runner and name it "Test"
3. Download the inkscape 0.92.5 installer exe from here
4. Click "Run Executable" in the newly-created bottle and select the downloaded installer
5. Proceed through the installation with all default options
6. Click "Finish" without running inkscape
7. Open terminal and run flatpak run --command=bottles-cli com.usebottles.bottles run -p inkscape -b Test and move the window to the left half of the screen
8. Open another terminal and run flatpak run --command=bottles-cli com.usebottles.bottles run -p inkscape -b Test and move the window to the right half of the screen
9. Close the window on the right half of the screen with "file > quit" (if window has no decorations)

The remaining window will stop responding to clicks. Attempting to force close it will also fail. The only way to remove the dead instance is to directly kill bottles (via sig-kill) in the terminal or system monitor.

Package

Flatpak from Flathub

Distribution

Manjaro

Debugging Information

Official Package: true
Version: '51.21'
DE/WM: plasmawayland
Display:
    X.org: true
    X.org (port): :1
    Wayland: true
Graphics:
    vendors:
        nvidia: &id002
            vendor: nvidia
            envs:
                __NV_PRIME_RENDER_OFFLOAD: '1'
                __GLX_VENDOR_LIBRARY_NAME: nvidia
                __VK_LAYER_NV_optimus: NVIDIA_only
            icd: /usr/lib/x86_64-linux-gnu/GL/vulkan/icd.d/nvidia_icd.json:/usr/lib/i386-linux-gnu/GL/vulkan/icd.d/nvidia_icd.json
            nvngx_path: /usr/lib/x86_64-linux-gnu/GL/nvidia-570-144/lib/nvidia/wine
        intel: &id001
            vendor: intel
            envs:
                DRI_PRIME: '1'
            icd: /usr/lib/x86_64-linux-gnu/GL/vulkan/icd.d/intel_icd.x86_64.json:/usr/lib/x86_64-linux-gnu/GL/vulkan/icd.d/intel_hasvk_icd.x86_64.json:/usr/lib/i386-linux-gnu/GL/vulkan/icd.d/intel_icd.i686.json:/usr/lib/i386-linux-gnu/GL/vulkan/icd.d/intel_hasvk_icd.i686.json
    prime:
        integrated: *id001
        discrete: *id002
Kernel:
    Type: Linux
    Version: 6.12.28-1-MANJARO
Disk:
    Total: 16677187584
    Free: 16677003264
RAM:
    MemTotal: 31.1GiB
    MemAvailable: 20.6GiB
Bottles_envs: null

Troubleshooting Logs

F: Not sharing "/usr/share/icons" with sandbox: Path "/usr" is reserved by Flatpak
18:47:30 (INFO) Launching with URI: None
18:47:30 (INFO) [Activate] request received.
18:47:30 (INFO) Bottles Started!
MESA-INTEL: warning: ../src/intel/vulkan/anv_formats.c:802: FINISHME: support YUV colorspace with DRM format modifiers
MESA-INTEL: warning: ../src/intel/vulkan/anv_formats.c:834: FINISHME: support more multi-planar formats with DRM modifiers

(bottles:2): Gdk-WARNING **: 18:47:31.129: ../gdk/wayland/gdkcursor-wayland.c:210 cursor image size (32) not an integer multiple of theme size (24)

(bottles:2): Gdk-WARNING **: 18:47:31.132: ../gdk/wayland/gdkcursor-wayland.c:210 cursor image size (64) not an integer multiple of theme size (24)
18:47:31 (INFO) Performing Bottles checks…
18:47:31 (INFO) Dxvks found:
- dxvk-async-2.0
- dxvk-gplasync-v2.5.3-1
- dxvk-2.2
- dxvk-2.3.1
- dxvk-2.5.3

18:47:31 (INFO) Vkd3ds found:
- vkd3d-proton-2.14.1
- vkd3d-proton-2.9
- vkd3d-proton-2.12

18:47:31 (INFO) Nvapis found:
- dxvk-nvapi-v0.7.0
- dxvk-nvapi-v0.8.0
- dxvk-nvapi-v0.6.3

18:47:31 (INFO) Latencyflexs found:
- latencyflex-v0.1.1

18:47:31 (INFO) Runners found:
- soda-9.0-1
- soda-7.0-9
- caffe-9.7
- lutris-ge-lol-p8-12
- wine-ge-proton8-26
- ge-proton9-25
- ge-proton9-7
- sys-wine-10.0

18:47:31 (INFO) Temp directory cleaned successfully!
18:47:31 (INFO) Bottles found:
- Test
- Common
- VPN
- ETL_SERVER

18:47:31 (INFO) Catalog dependencies loaded
18:47:31 (INFO) Catalog installers loaded
18:47:31 (INFO) Catalog components loaded

(bottles:2): Gdk-WARNING **: 18:47:33.344: ../gdk/wayland/gdkcursor-wayland.c:210 cursor image size (64) not an integer multiple of theme size (24)

(bottles:2): Gdk-WARNING **: 18:47:34.866: ../gdk/wayland/gdkcursor-wayland.c:210 cursor image size (64) not an integer multiple of theme size (24)

(bottles:2): Gdk-WARNING **: 18:47:34.866: ../gdk/wayland/gdkcursor-wayland.c:210 cursor image size (64) not an integer multiple of theme size (24)

(bottles:2): Gdk-WARNING **: 18:47:34.867: ../gdk/wayland/gdkcursor-wayland.c:210 cursor image size (64) not an integer multiple of theme size (24)

(bottles:2): Gdk-WARNING **: 18:47:35.352: ../gdk/wayland/gdkcursor-wayland.c:210 cursor image size (64) not an integer multiple of theme size (24)

(bottles:2): Gdk-WARNING **: 18:47:35.359: ../gdk/wayland/gdkcursor-wayland.c:210 cursor image size (64) not an integer multiple of theme size (24)

(bottles:2): Gdk-WARNING **: 18:47:35.502: ../gdk/wayland/gdkcursor-wayland.c:210 cursor image size (64) not an integer multiple of theme size (24)

(bottles:2): Gdk-WARNING **: 18:47:35.502: ../gdk/wayland/gdkcursor-wayland.c:210 cursor image size (64) not an integer multiple of theme size (24)

(bottles:2): Gdk-WARNING **: 18:47:35.516: ../gdk/wayland/gdkcursor-wayland.c:210 cursor image size (64) not an integer multiple of theme size (24)

(bottles:2): Gdk-WARNING **: 18:47:35.543: ../gdk/wayland/gdkcursor-wayland.c:210 cursor image size (64) not an integer multiple of theme size (24)

(bottles:2): Gdk-WARNING **: 18:47:35.888: ../gdk/wayland/gdkcursor-wayland.c:210 cursor image size (64) not an integer multiple of theme size (24)

(bottles:2): Gdk-WARNING **: 18:47:37.402: ../gdk/wayland/gdkcursor-wayland.c:210 cursor image size (64) not an integer multiple of theme size (24)

(bottles:2): Gdk-WARNING **: 18:47:37.587: ../gdk/wayland/gdkcursor-wayland.c:210 cursor image size (64) not an integer multiple of theme size (24)

(bottles:2): Gdk-WARNING **: 18:47:37.588: ../gdk/wayland/gdkcursor-wayland.c:210 cursor image size (64) not an integer multiple of theme size (24)

Additional context

To set up a file association for svg to run the bottled version of Inkscape, I used a .desktop file with the following program and arguments:

Program: /usr/bin/flatpak Arguments: run --branch=stable --arch=x86_64 --command=inkscape --file-forwarding org.inkscape.Inkscape @@ %F @@