I have finally found that in Options-General-Performance you can select how many CPU cores you want to use for ripping. I selected "1" (was "all") and now all tracks are ripped in the correct order (at least with one sample CD).
Interestingly enough the time to rip didn´t change significantly, probably the CPU isn´t the bottle neck but the disc drive.
For me this issue can be considered solved.
Get answers about using the current release of MediaMonkey for Windows.