I had a very similar problem, an old PS2 keyboard connected through a ps2->usb adapter and after I remapped the capslock to ctrl in Windows (both XP and Win7) I could never get the second control modified keystroke to be taken as a control character. What I found was after I released the first control modified character I had to release and re-depress the capslock key in order to send another ctrl character.
I had edited the registry entry for HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Keyboard Layout and added a Scancode Map entry
I knew that the original ctrl key worked fine on the PS2 keyboard, as it would allow multiple ctrl modified chars to be typed without re-depressing the ctrl character. I also knew that the capsLock key when remapped to ctrl char worked fine as a ctrl key when the keyboard was connected via a PS2 port to the computer. So my conclusion was that the USB converter or connection was failing to pass the multi ctrl keystrokes.
Eventually I tried a USB keyboard connected to the USB port on the PC and I found it works fine, either with the original ctrl key or with the remapped caps-lock key. With a working solution I did not do any further research but it seems conceivable that the problem is in the PS/2 -> USB converter I was using.