Not sure I can help but what version of the firmware are you running? 9.57 is the newest version and can be downloaed here:
It's beta software but the guys from EagleTree are recommending updating to it if you are having troubles.
Also, which versions of eLogger, GPS, and altimeter are you using?
billpa from EagleTree drops in on the support forum about 2x a week and answers questions so you might try posting the question down there:
I've checked through the first couple of pages of questions and there are a couple that sound similar to yours but they've all sort of faded out without a real explanation as to if the problem got fixed or not. In one case billpa asked for the log files and it may have been a defective unit.