I'm not much experienced on the server settings but I think in case of dynamic cal allocation it may use the CAL for other end users too but that case will arise if you have session CALs exhausted.
Maybe you can give it a try by disabling the dynamic CAL allocation.
Another thing is, When you said:
"Whenever I try to open a workbook in server, I am able to open it up just fine as a user (meaning I can't open or edit scripts)."
Did you mean that you are able to lease a license from the Server? in that case the connectivity should be fine.
Are you using Alternate User option or any other option while connecting to the Server in "Open in Server" mode.
If possible can you send me a screenshot?
When I said that, I meant that I am able to look at the workbooks listed on the server and access the AccessPoint page, and I can run the apps like a user. But It doesn't give me a licence and I can only look and use the app, not modify or move it. If I take the .qvw and open it just like a normal workbook file instead of opening in server, then it gives me the error that I can't open workbooks created by other users because I have the personal edition.