Hi Roland,
The gap of 5 minutes for instances that time out is due to the Maximum Throttling Delay setting in message processing (or publishing) located in the BizTalk Host properties’ Advanced tab section (the default setting is 300,000 milliseconds, or 300 seconds or 5 minutes). You might want to adjust these settings to boost your BizTalk server’s performance, here’s an MSDN article for more information:
http://msdn.microsoft.com/en-us/library/aa559628.aspx
With regards to seeing the number of running instances increasing, make sure that these are not orphaned BizTalk instances. Here’s a blog on more details about this issue (with a link to download a hotfix and some tips):
http://moriahsoft.com/ImadE/post/2010/05/10/Purging-Orphaned-BizTalk-Instances.aspx
I hope these help in resolving your issue(s),
Daniel.