COM2 works on 2.6.21 but not on 2.6.29?
 

We have a GPS receiver connected to COM2/ttyAM1. It works on
2.26.21, but not on 2.6.29. It's settings are 4800 8N1, and stty gives 'the
same' flags. Appears to work ok with minicom, but we cannot write to the GPS
receiver on 2.6.29, and we get "ttyAM1: input overrun" during prolonged use
reading NMEA strings from it. It's fine on 2.6.21.

What is telling is this:

Start reading NMEA strings via minicom, no overruns.
Start a user space process then that writes a little to SD, pdflush becomes more active, then blam, overruns /dev/ttyAM1 @ 4800 baud, and no overruns on
/dev/ttyAM0 @ 115200 baud. How can that be?!

Is pdflush using IRQ5 or competing with us for some other resource? THANKS

Are these custom built kernels, which Debian release/branch are you running?