I have difficulties to understand that you have all the mentioned problems, I wonder whether you had the same with WM5. Probably something went wrong while you flashed the ROM.
I'm using the Newplow 38 version with SDHC support since August 08. GPS was updated before. This is important as the GPS hardware settings are changed when updating (flashing) the original WM5. This is a precondition when flashing NP38 with GPS support.
All my navigation SW works fine (NavigonMN6, Destinator6 Europe and Australia, Vito + GPS-meter) The GPS programs work fine, not better or worse than with WM5.
3 different 8GB SDHC cards work fine. Compared to 2MB standard cards the only deficiency is the fact that all GPS applications must be turned off before hibernating, otherwise the application freezes when waking up.
Hibernation works and the power consumption is lower, the battery lasts about 20% longer.
Connection to Wifi networks is easy.
The system runs much more stable.
For a short period I have used also the Jan09 Version of NP WM6.1 . I didn't like it, I couldn't find any important improvements over ver. 38 WM6.0. Skype made some problems, so I went back.
With hindsight: It were only the few minutes of worry when flashing th+ N560, everything after that was/is fun.
wishes from Queensland Australia