That's strange indeed. Here are some troubleshooting hints:
Could you please make sure that you do not have multiple instances of the pgdn daemon running (“ps | grep pgdn”)?
Also, make sure that you have none of the key layout modifications the Wiki recommends
in your gpio-keys.kl.
You can use the evtest
program (from the original pgdn distribution) to check which events are generated by each of the input devices. Use like so:
where eventX is one of the event* files in /dev/input (try each one). (Remember that you need to copy evtest to a partition from which you can run code: /data or /system, not /sdcard.)
You are correct that “profile SOME.APP.ID 0 0” is used to disable pgdn's default mapping of the Left / Right keys to Dpad Left and Dpad Right for one app. Use this for apps that are natively enabled for the PRS-T1 keys.
You say that you've modified the dot.pgdn file. But you do mean the /sdcard/.pgdn file, right?