I had the same issue using Perfect Keyboard from the Play Store, both on Stock Rom and on Viper Rom. Uninstalling and reinstalling didn't work, wipe data didn't work, even showed the issue right after a clean install (full wipe). Don't know the cause but I begrudgingly switched back to using HTC stock keyboard and no problems for over a month. I miss using the volume keys for moving the cursor, but I hated this issue even more...
Perhaps let the dev know and see if they can isolate the issue, otherwise use a different keyboard? Sorry can't help, but you're not the only one that's see the issue!
Sent from my Viper 2.0 HTC One
AT&T HTC One
ViperRom v2.0.0 (stock kernel)
HBoot: 1.54 - SOFF, SuperCID