The Win UAE is about 30 % slower than the Linux UAE Version.
Highly unlikely.How are you measuring it? Did you create the configuration from scratch? (moving "high end" configurations from non-WinUAE to WinUAE or vice versa usually does not work very well because of differences in supported "expansion" features etc..)
Usual issue in WinUAE "high end" JIT modes is too high activate priority (normal or below normal is good) and/or CPU idle adjustment is needed (2-3 steps to right is ok usually)
