I tried to replicate this without any success.
What exact dimensions were you using?
My EEby... tools are robust and work if the initial objects selected and subsequent input comply with the tool's needs etc, so I can't see what's going wrong.
Dis it occur during picking or during the latter stages - like reversing faces or exploding the extrusion-group ??
If you can't reproduce it then it's probably a one-off glitch within Sketchup itself...