Okay, first, stop changing things. Too many changes will only make it confusing. Make your changes in bulk, then check them all in at once.
Secondly, changes don't take effect instantly. It may take several hours for a change to show up.
Third, if you're using tagged versions, then the only thing read from the trunk will be the "Stable Tag". Everything else comes from the tag directory. So changing the readme.txt in trunk won't have any effect at all unless you change the tag.
Finally, all changes matter. There's no difference between PHP and TXT and anything else. So you can just stop trying to figure it out.
People continually doing crazy stuff like this is what causes it to get horked up in the first place. STOP IT. If you think it's behaving weird, then stop screwing with it. Email me which plugin you think is having the problem, and then I will investigate and either fix the problem or tell you what you did wrong.
Either way, you cannot debug the thing. Stop trying.