For the past couple of version I have been dealing with the issue of the FTP saying "collecting files" when I try to upload changes to my server. It will ussually hang for 10 seconds or so and then transmit the file. Sometimes it does this and other times it uploads instantly.
I use Site Ground and I have contacted them and they said everything look find on their end.
If i use a thrid party FTP software it always connects just fine so I don't know where to begin with this issue.
I am using PHPstorm 10 on El Captain, but it did the same with version 8 and 9.