I had those issues, mainly playing music out of JRiver (not quite as often on Foobar). For sure, you will want to make sure you have the latest Firmware installed on the micro. When I did that, it solved the issue MOST of the time. Go to http://highresolutiontechnologies.com/support/, download the Upstream/UpstreamHD app and USB View app, then download the Firmware package. When you download and unzip the firmware, look for the file uS_1v3.bin, thats the file for the microstreamer; uS is meant to be read 'mu'S as in the greek letter 'mu,' which is used in science to denote 'micro' measurement, sorry, couldn't resist a science blurb :)
Apparently the HRT needs to be able to draw a lot of current through USB to work properly: so make sure you are plugging it in to the USB port that has the most power, and if you are using a laptop (or some other portable device) make sure it is connected to the wall outlet. This helped out alot.
Alot make sure you have a solid USB cable, I beleive the HRT comes with a monoprice cable included, but for whatever reason, it's always fit kinda 'floppy' in my USB ports. So you might want to order a new one from Monoprice (I havent ordered a new Mini-B from Mono, but have gotten Micro-Bs from them that do fit very snug).
Finally, make sure your audio player is properly configured. I found JRiver to be at odds with the HRT more so than Foobar. Most of this wasn't issue though once I upgraded the firmware, so I think you should start there, but definitely recheck your your player's settings. I took some advice from this thread: http://forums.stevehoffman.tv/threads/got-the-new-hrt-microstreamer.308955/
Hope this helps, I did all these things and it made for a more trouble-free HRT micro playback.