This probably isn't for everyone but I have found a workaround for subl's flakiness:
If you use the --wait option the tool works every time.
Using this from the shell causes some oddities (luckily that isn't my use case) but you can mostly work around them by putting the command in the background (with an & at the end of the line). You'll probably have to write a fully-fledged shell script to get this working seamlessly as it's beyond the scope of an alias or symbolic link.
I have the same problem on OSX 10.9.3 with ST3. I had ST3 open with 2 files opened. Using subl .zshrc_backup ST3 window came up but the file was not opened. Instead one of already open files was shown. Executing just the same cmd again opened it eventually.
For completeness: I am using zsh and have seen this behaviour both with the Oh-my-zsh and prezto frameworks for setting up zsh.