I might be a bit late for this thread, but I've used Google Base in the recent past.
I had exactly the same problem - this issue was this: There's a US and a UK version of Google Base. IIRC, you can actually log into both versions using your same Google account. But not at the same time.
If you can see your products in Froogle, then you've probably uploaded them in the UK version of Base.
If you later can't see them, you're probably logging into the US version by mistake. Try logging in via:
http://www.google.co.uk/base/