Jalview launch/web services issue when behind proxy

I've run into two problems when running more recent versions of jalview on debian systems but only behind the proxy at work. Dealing with proxies is a consistent problem for me with many programs on Linux; this may be user error, though I have all appropriate environment variables set and most software runs and connects/autoupdates just fine.

First issue, upon first install, the clustal-colored progress bar during splash screen for "launching" would get stuck and jalview would half-hang. I cannot remember how I resolved this, but I somehow managed to turn off options for checking for updates and web retrieval services. This allowed a normal start up without issues. (Come to think of it, this was major enough that it almost blocked my using it, I'm sorry I can't remember how I did the workaround)

Second issue: even though various services are unchecked, the main jalview window has a progress indicator for connecting to services which is stuck at 0 and doesn't ever progress. All other functions are a-ok, so it's pretty minor, just annoying.