What error message do you see, precisely?

Shot in the dark: you may turn off logging in the analytics settings.

you see a series of errors involving these 2 tables from mysql's error.log (with db name edited out):

130713 8:00:05 [ERROR] /usr/sbin/mysqld: Table './xxxmdb/xxx_sessions' is marked as crashed and should be repaired
130713 8:00:05 [Warning] Checking table: './xxxdb/xxx_sessions'
130713 8:02:48 [ERROR] /usr/sbin/mysqld: Table './xxxdb/xxx_hitlog' is marked as crashed and should be repaired
130713 8:02:51 [Warning] Checking table: './xxxdb/xxx_hitlog'
130713 8:03:03 [ERROR] /usr/sbin/mysqld: Table './xxxdb/xxx_hitlog' is marked as crashed and should be repaired

b2evolution cannot do anything to crash your tables. When MySQL tables crash, it is generally when MySQL dies (bug, out of memory) or if a computer/sever is switched off without properly shutting down the system.

This is not really a b2evolution problem.

Note: you can repair your MySQL tables with phpMyAdmin.

Beyond that, what is your "home server"? If it stalls when running b2evolution v5, maybe it's not powerful enough? Is that possible? How old is that machine?

The server is 2-3 years old, on 24/7, currently running Ubuntu V12 with 1.5G memory. It's not as powerful as professional web hosting servers, but it didn't have the stall problem prior to the upgrade, hence I thought it's probably related to V5. Maybe something is using more memory than prior versions?

Yes, I'm using phpmyadmin to access and repair those tables.

Currently my work-around fix is to add a cron job to restart apache every hour. This is probably not the correct fix but the frequency of stalling and repairing table has reduced.

Sometimes it's also a bug in MySQL. Make sure you keep it up to date with latest fixes.