The .exe from SourceForge was updated in December whereas the jar file from KoLmafia.us is built from the most recent code available. It is possible that changes to KoL that are reflected in KoLmafia (new items, etc.) could account for the difference. But it is also possible, if this is a memory issue, that Windows allocates more memory for the .exe than the .jar.
I have solved the scaling issue and commented on it KoLmafia.us. Try searching on HDPI or DPI but it is basically the reddit solution. It can be applied to the .exe with a little digging but, to be honest, I'll never run the .exe and it is not worth the effort.
Generally Java only does garbage collection when it needs memory or there is a lot of garbage. So one quick test would be to try and tell the operating system to start Java with more memory. I cannot trivially find the default settings for Windows or how to change them at the OS level, but if you open Windows cmd, change to the directory that contains the jar file, (and presumably all your mafia files) and type
that will run mafia with a known amount of memory. You should use change the jar file name parameter to match the version you have. Depending on how you implemented the HDPI fix you may find this launches tiny screen mafia (in which case find java.exe and add a manifest file there, assuming you understand the fix). You should not have to change the 2048 unless you get an out of memory abort or the operating system complains it can't allocate that much. The key is the 256. If you really have a garbage collection problem then increasing "the 256" should result in less GC and possibly address your problem. I suspect the 256 might be higher than your system's default is so try that first.
java -Xms256m -Xmx2048m -jar KoLmafia-18577.jar
It is good to know that /count is a culprit. What is it supposed to do? I have a vague recollection that slash anything in the gCLI invokes a chat command that is "native" to KoL but since I take a perverse pleasure in ignoring all things chat as much as possible I will plead ignorance :-)