Heinrich,
Although I do not have the problem you are experiencing, I am keeping an eye on this thread is case I do have a similar problem in the future. I hope you can get an answer soon to solve your immediate problem. Aside from your cup of coffee example, from my experience, the Base Report Generator can take much more than 60 seconds to render a large report. I am not sure how Base collects the data for a report, but if it does so a record at a time, then your server would time out way before the report is finished! I would think that the best case would be that the constant reconnects would slow the Report Generator even more.
Since it sounds like your system worked before LO 4.2.x and I suspect you where using the Oracle MySQL-connector-java, as I am, there may be a way to replace the new native connector with the "tried-and-true" Oracle connector. That would get you up and running again until more information on the native connector is released. I have no experience with this, but it may be an option for you, if it can be done.
Good luck.
Girvin