Hello Johann! I guess the only way to get millisecond scale resolution is using the second timer of the etrax processor in a kernel module. I wrote a driver that's polling input pins at a frequency of about 10 kHz, using the second timer. It needed a recompiled kernel (disabling of fasttimers to get a free interrupt), but wasn't that difficult after all. If writing a kernel driver is an option to you, I can give you some example code for accessing io in an interrupt service routine.
Best regards Dietmar
