Hi I just tested this on my computer and it works perfectly, following settings:
A pulse that repeats every 100 ms
total time was 8 mins and 20 seconds, which equates correctly.
The question I have for you is why do you want to capture all 5000 waveforms?
You can still capture all waveforms but setup a mask and then show only the waveforms that have failed. Have a look at the video below:http://www.picoscope.tv/general/mask-limit-testing.html
With regards to your question about the SDK you can only have one time base for all channels.