Turn off all cacheing in both admin panels and clear any cached files. Then, you need to figure out what you are trying to do and get organized.

You should also make sure that bot installs are using DIFFERENT databases.

You should move one install out of the catalog dir and put it in a completely separate dir like shop or catalog2, alongside your existing catalog dir, not below it. This way, you MUST change the path in the first branch in order to see the new site, and there is no chance of mixing paths.

It also allows you to have 2 separate sites with the EXACT same dir tree structure, with different names. This is great for comparison. If one isn't working, you can look at the other one for help (if it is working, of course!).

A little forthought goes a long way in making your life easier. This is completely avoidable.