It's been my experience that certain soundcards report their position inaccurately, leading to exactly the issues you describe. The fact that a restart seems to help further indicates that the soundcard driver is misbehaving.
It might be a tricky thing to debug if you don't have multiple soundcards (and, really, only us freaks do) but you could try messing around with using different driver modes in the audio hardware configuration dialog. It's all down to your particular sound card and its drivers.
Sounds like you're dropping out from sound card issue or system resources...things to check/try:
1) check sound card latency: it could account for this or possibly overcome it, I might suggest increasing the latency under preferences > audio hardware and see if this improves your performance. Do you know what kind of sound card it is?
2) Check resources: Even by doing that you may not resolve the problem if the RAM, CPU and/or disks are busy or taking hits from other applications. This can create negative impact on the real time performance needed for playback. Disk I/O bottle necks are a common cause of latency and drop outs (on any audio system). So maybe also check your system resources and see if you're maxed on memory (and thus swapping memory to disk).
3) Move temp or audio to a different drive than system if possible.
4) Disable or shutdown unnecessary services or applications when working with audio, generally it's not an issue, but if you have many things installed that are taking resources, some application will end up the "victim" or show signs of problems.
5) Virus scanners can be part of this problem too, so try this w/o real time file checking on (temporarily).
there's lots of possibilities here, but I think the above stuff is a good place to start.