If you rename the .bat file to WinUAE.exe, you have to rename the original WinUAE.exe too. Rename WinUAE.exe to WinUAE12.exe and change the .bat file the following way :
Code:
WinUAE12.exe -norawinput %1 %2 %3 %4
The extra '%' parameters are in there just to make sure that this is not the problem (might also be possible that this was the only problem in the first 'version'). If that doesn't work I really recommend that you switch to 1.5.3, because building workarounds that cause new problems for an old version isn't really a good idea. I can (to certain degree) understand that you want to keep 1.2, but as you can see this old version also has side effects on Vista. Well it's your choice