Some programs (namely mIRC and SoulSeek), totally vanish from the OSX Doc when I click the 'minimize' button on the Windows - Even though Windows is reporting that the program is indeed running. How do I change this?
Apps are removed from the Mac OS X Dock when they're closed. Maybe those Windows apps are made of two processes - a UI that Parallels shows as a Mac app and which closes when you click minimize, and something else which Windows shows as still running? Check the Windows Task Manager? Does the Windows app show up again in the Mac dock when you un-minimize it?
Nope..it just closes and I'm unable to get it open again until I go into the resource monitor (within Windows) and force that process to close.
So minimizing is causing the program to crash which causes it to be removed from the Mac dock. This sounds like a bug with those programs and not with Parallels Desktop... What version of Windows are you using? Do those programs work normally if Parallels Tools is removed? Do you have a Boot Camp setup and if so, do those programs work normally when you boot into Boot Camp using the same version of Windows? You may need to get support from the developers of those programs.