I had a similar (but strange) problem yesterday after installing (via Update prompt) iTunes 12.1. Everything looked OK but I found that my wife's iphone 4S wasn't detected by iTunes, but strangely my iphone 4S was. Checked cable (same cable), checked connecting port on both phones, everything OK. Both phones were detected by Windows (8.1 64 bit). Decided to reboot both phones and the PC. Made no difference. However, sometimes MY phone wasn't being detected either.
Finally I deleted iTunes following this set of instructions http://support.apple.com/en-gb/HT1925 and reinstalled iTunes from a fresh download. Everything now working OK.
Make sure you follow the sequence of uninstall processes before reinstalling.
Hope this helps.