I had all kinds of trouble. Background kept returning to white, channels wouldn't stay, only addon msgs were being shown, fonts returning to small. Slash commands were getting through but were not showing in the chat frame nor was general chatter. You name it it was driving me nuts. Fought with it all day. Finally tried the deleting any saved variables/caches with prat or chat in them and the addon itself. Closed down wow and resarted. Had same problems. With auctioneers swatter coming up with 5 for 6 errors everytime on a restart or reload I didn't pay close enought attention. This time I did. An error with CallToArms. Hmmm.... I thought and promptly disabled it; reloaded and low and behold the std wow chat was back to normal. Reinstalled Prat and everything appears to be working hunky-dory at the moment.
Long winded I know. But, it just goes to show you that even though and addon is working (CTA in this case and working well) it was frackin up Prat.