In contral center, I have some of my apps such as agent desktop and others with reddots with x's in them. Is my CRS corrupted? Do I need to re-install or can I adjust the configs to fix these issues? The version i'm using is 4.0
Your CRS installation is corrupted. The best solution is reinstall.
I think that, first, uninstall your current CRS deployment and then install CRS again. If oyur scripts and prompts are stored in the CallManager Directory, when you reinstall you only have got to select the LDAP profile and you will have your full configuration.
I was actually having the same issue with my CRS Engine last night. TAC directed me to some registry keys to fix the problem. Now, I'm not sure if this same fix applies to the components you reference but it's worth checking out. Basically, there are 2 keys in the registry that affect this. One that is a counter and one that is a flag that will not allow the service to start. If the counter reaches a certain threshold, the flag will be set from 0 to 1 and the service won't start. He simply had me change the flag back to 0 and the counter back to 0. Unfortunately, the engineer didn't put detailed instructions into the case note or I'd share exactly where these were. Again, this may be completely different but it's worth checking into.
These are the paths to get to each CCX logs through CLI. They may be helpful if you are having issues accessing RTMT or downloading logs through it.
If you want to download them you have to prefix "file get " and you can add one of the options (re...