@Andrew-Jaffe it is indeed a permission issue, but not in the regular filesystem permission level, but in Apple's OSX sandboxing kind of way. Basically, Manuscripts is allowed only access to the files and folders you have explicitly selected to open / save to.
Sandboxing is excellent from a security perspective, because you can be sure that Manuscripts does not delete or read files on your disk that you would not want to, or indeed you can be sure that it only accesses the system resources it needs and has no capacity to break your privacy (for instance it can ask for access to a printer because it's a writing tool, but it cannot access your geographical location). Basically, even though you as the user have access to a file, Manuscripts does not before you've given it.
The way OSX enforces these sandboxing rules is less than excellent, because for instance in this case, you indeed need to first select the TeX file you want to import… but that is not enough for files that reference for instance images, bibliography data or other TeX files. That is why we have a dialog then requesting access to the containing directory. This flow is the best we could come up with, whilst still keeping the app securely sandboxed. There's a few other cases like this (same deal for instance with Markdown importing). However, I get the feeling the text we use to describe what's asked could still use improvement (it's sort of an implementation detail that it is asking for a permission).
Now, your specific symptoms are likely explained by something else: the request for accessing the folder works, and it will indeed not request for access to the folder again once you have done it once (the app holds on to some information that then lets it access the file or folder once first permitted)… but then something after that fails. It could be due to some unexpected content and an example should help us get it sorted.
CEO & Co-founder of Manuscripts.app Ltd