From my experience, once you install Windows (on the same drive, separate partition) as OS X there isn't much you can do. Gringo is correct in saying that Windows is corrupting the boot loader. In 8 years, from XP to 8.1 I have yet to find a solution.
My suggestion is to back-up the OS X partition and start over. When you install Windows on a separate hard drive ALL other drives containing other OSs must be disconnected (optical drive and drives used for storage are ok) or Windows won't install. Often the installer will give a warning prompt shortly after the process starts and exits. If it does there is a good chance that the HDs containing other OSs will get corrupt. The same goes for installing on the same HD but different partitions.
Here is what I have always done. I gave up on trying to fix things years ago and just went with a fool proof method.
1) Format the HD into 2 partitions; 1 HFS+ the other Fat32 (or NTSF)
2) Install Windows FIRST on the 2nd partition
3) Install OS X on partition 1
4) Install Chameleon/Clover/Chimera
You can try to install Clover on the EFI partition (of the hard drive or from USB) and boot from there. Of course you need an UEFI motherboard for this to work. On that note, if you have the know how you can try reformatting the EFI partition, as well as setting the OS X partition as active. There are many guides here with the info you need.