Why don't I get a selection window with SSD?

I recently replaced the optical drive with a Crucial SSD. Most everything seems to work properly and I am still testing before reformatting the HDD. My goal is to use the SSD for applications and the HDD for storage/docs, etc. My big issue right now is with uploading pictures and audios to my church website that uses Fat Cow for hosting. I click on the upload button, then click on browse to find the file I want to upload and nothing happens. It just sits there and a selection window never opens. I have tried both Firefox and Safari with the same non-result. If I reboot to my original HDD, everything works fine. Both drives have the same updated El Capitan running on them. I contacted Fat Cow and was told everything is fine on their end and it is an issue with my system. Please help! Thank you.