This is a solved problem, just recording.
I changed the Device settings >> Log format checkboxes, and magically the program seen only 300 of the 6000 trackpoints recorded. Since there were "bad entries" in the conversion I thought it's some log format error, or data interpretation error.
As it turned out (after God Himself [mdeweerd] asked and told) somehow the old settings in Filters (mainly trackpoint filters) were too strict, which worked with the old settings but filtered nearly everything afterwards. Checking allmost all the filters (to include everything [of course not _everything_, since I wanted to discard pos without a valid fix for example]) made magically available all the 6000+ points again.