I just answered in a WinMo 5.0 question, but it works for 6.0 too, so I will send it:
In http://forum.xda-developers.com/showthread.php?t=549675 you will find a driver for the emulator, which installs a RAM disk, which for the emulator is considered as an external memory card, but does not suffer from problems with displaying the folder. I checked with the SD Compact SQL file stored in RAMDisk and it works like a charm. I used it as a 64 megabyte drive, but presumably it can handle up to 256 MB.
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