I had a similar problem occur with my points nearly 2 weeks ago and I have yet to receive an answer. Apparently the computer "ate" about 100 of my points in early April. Every MS CM I spoke to insisted I used my points in some way or another. It was (and still is) very frustrating!
I had 100 pts transferred into my account at the beginning of the month and they can see them being transferred in, but then they're just gone. I've spoken to several supervisors, some more helpful than others.
One actually tried to convince me that I used them on a reservation I booked in December. Another one told me I used them already

ummm....then WHY am I trying to book a trip for November??
I had 40 points (07 UY) in holding that I'm planning on using in August and they actually took those 40 points out of holding, put them in 08 and banked them. All of which they tell you is not possible to do, so I figured they must KNOW they're wrong....
I'd rather them say something like, "Look, there's a computer error somewhere and we'll fix it", than try and convince me that I used them or tell me they're doing me a favor by letting me use points that were in holding.
Very frustrating...I hope they get it sorted out soon
Phone calls have gotten me nowhere, so I emailed yesterday.