Regarding your question on IRC, there is a retry-attempts setting for eopkg (you can use it from the command line):
-R [--retry-attempts] arg : Set the max number of retry attempts in case of connection timeouts
The default is 5. Not sure if one can also set the timeout without modifying the code directly.
In general it sounds a lot like the issues people had with proxies from time to time, but you mentioned on IRC you aren't behind one, right?
