Sorry, but you totally lost me when you said you "aliased" things.
What the heck does that mean to you?
First, I'd suggest triple checking that the path is set up correctly in your CSH mapping. I know you said you already did, but I've been caught out by that a lot. So go through character by character and make sure it's right.
EDIT: And make sure you have the correct ID from the application, and that your developers have the correct/latest version of the map files.
Another thought is that the hhp file contains "old" hard-coded paths. Take a backup of the hhp in case anything goes wrong. Open the hhp file in a text editer, find the [MERGE FILES] section, and make sure the paths to all the chms are relative paths and also correct. Delete any extra rows. Rebuild your chm.
I can't offer a permanent solution, so you may need to do this each time you generate or at least regularly - I could never figure out why the paths would get (re-)added.
As it's a different chm file, it's possible that somehow that file fell afoul of Microsoft security measures. Try right-clicking on the chm, selecting Properties and see if there is an Unblock button. If there is click it and see if that fixes the issue. I'm not sure how you would solve this permanently, if the chm is being downloaded/copied from the internet or opened from a network drive. If it's being shipped with an application, then making sure it's unblocked before it's packaged with the application "should" work.
I also found this old thread which may or may not help:
The registry keys would be a per computer solution, although it's possible your application might be able to set them - you'd have to talk to your developers though.
Captiv8r I believe 'aliased' means mapping CSH IDs.