Dropbox very occasionally suffers from the same thing, but thanks to a feature in the Mac app, it is very easy to resolve.

I am using GoodReader now, and while it has a decent feature set it's really painful to use. Just a bad UI, and very ugly. I could live with all of that if it had one key feature, though. So what I am ...

DropBox installer app only gives option to sync with my C drive... not enough space. I need it to install/sync on D instead. WTF? How the heck does it NOT give you this option?