Forecast File Inputs not copying?

[Mkrig24]

I am running an MSE using sablefish stock assessment files, which have catch inputs specified at the bottom of the forecast file that cap catch at the ACLs set by council in the first two years of the model. When the model runs outside of SSMSE these inputs correctly cap the catch, but I noticed that inside of run_SSMSE, when the forecast file gets copied to _EM_init these input values aren't copied over, and the catch ends up being significantly higher.

becomes

Is there a way to make sure these inputs are copied over? Or another work around to get catch specified correctly in these first two years?