.... [error] File not found: /webroot/site/undefined .....
I've got a strange feeling the problems are associated. I'm asking for the right script src pathways without a doubt.
Any reason the heck "undefined" could be asked for?
Information: PHP script, customers are embedded IE8 programs.
If you absolutely call the right script URIs (“script src paths” while you say) the issue are only able to lie inside your apache configuration.
Look at your rewrite rules etc.
You may even wish to look at your access log, whether strange/wrong pathways/Web addresses were known as.