Apps showing up twice in open with menu

Hey all.

When I right click on a file (lets say a photo) and go to the "Open with" contextual menu. I'm getting duplicate app entries, ie: two photoshops, two google chromes etc.

I know there is a terminal command to clear this out, but the problem is that it happens on every single reboot.

I think the problem may be related to the fact that I have 3 drives, one internal that I use as a carbon copy cloner backup drive, one external which I run my mac os off, and another external that I use as a time machine backup.

I'm sure i'm not the only person in the world that has a set up like this so has anyone else experienced this and found a fix? It's terribly annoying and only one of the two duplicate programs in the open with menu actually work. So you have to either guess correctly the first time or go through the process twice.

Running the terminal command and killing finder on every reboot is tedious. (i also tried just creating an automator app to run the command on startup then kill and relaunch finder. It doesn't work though because I believe it's happening too quickly or something)

Thanks for any assistance

 

Thats the command I was talking about in my post. It works but the duplicates return on every reboot, thats the problem :/

 

1) When I said "reboot" I also meant startup. I turn my computer off at night and turn it back on in the morning for work.

2) The problem is that the clone drive is the internal drive. I run my operating system off an external thunderbolt ssd

 

Good question. No, not all apps. For instance if i right click on a png and go to the open with menu it shows two google chromes, two photoshops, but only one color sync and one pixelmator etc. It also beachballs for a bit before showing the menu.

I run my OS off the external ssd. I just set it to my startup disk, thats it. Just once. I clone a daily backup of the aforementioned ssd to the internal hard drive in the iMac once daily.

This seems like a punishment for being smart and backing up
Thanks for all the advice thus far. Would be great to get to the bottom of this

EDIT: I resolved this issue by just not backing up applications with CCC or time machine. I instead just backed up important files like documents, programming source files etc. Not a fix as such, but a smarter approach