It really was the compatibility mode, thank you so much!
To be exact, C&C95.exe was running in Windows 95 compatibility mode, once I uncheck it it runs normally and fixes the memory bug. Although the CCConfig.exe automatically enables compatibility mode in the C&C95.exe when saved.
Didn't try it with the mini mp version yet.
But now I happen run across the issue, that the mouse is available in windowed mode, but it's also running through my desktop and I can't click anything with my mouse... CCConfig.exe doesn't seem to have an option for it, but the ddraw.ini does. mhack needs to be set to true instead of false.
Thank you again. It works fine now.