I'm guessing (please note, guessing) that it has something to do with the creation of the manifest file on the cache, don't think it's directly related to .htaccess at all.
Judging by the path you install is, i'm also guessing it's in a server with domain reselling and probably has a software managin domains (stuff like cPanel, Plesk, etc), so, my first course of action would be to try to figure out where SS is trying to write the cache (which path) and see if it has permissions to do so.
Another thing it can be, (happens) is due to the upload the file got either corrupted (ManifestBuilder.php) or changed due to the transfer type (binary/text), another thing i would do, which would be the first thing to do actually, would be to see the file contents and compare it with your local version.
I've just checked my ManifestBuilder.php and i've noticed a constant called TEMP_FOLDER which is set with getTempFolder() from Core.php
The function calls several functions which might be blocked due to the use of safe_mode in PHP (which is most likely on, being a Hosting server) worth a check also.