I had a small ray of hope this morning when my PC told me there was a new version of iTunes (12.3 - I did check last night as I had 12.2.2.25 but was told that was the latest!) but no, I had updated some apps on my iPhone and they have not transferred to my PC (tried transferring purchases but that just re-transferred items I had already moved to my PC when I bought them).
I've asked friends on Facebook if they are suffering the same, so far only two responses - one Mac user, one Windows neither of them with problems so it's not a general problem.
So just in case this info is of help
I use manually manage for my devices
I have windows 8.1 which is full up to date with all windows updates
My Apple devices are all on OS9
I do not use the Apple Cloud other than to re-download things I no longer have on my computer (which is rare as anything not on there is on a back up hard drive).
I sync via PC, i.e. connect a lightning cable - I don't use wi fi synch. (Will test out wi fi synch this evening when I have time to do so in case that does work but if anyone on here uses that already let me know so I don't waste time).
Once I have the time to do it, and if no other solution appears, I may turn on Cloud and see if that makes a difference.
Edit - note this is not just an iPhone problem, it's all my devices and there's at least one other post in the iTunes for Windows thread and again when I have time I'll see if there are any more with this problem).