It seems that Remote Control 4 isn't taking notice of the archiver engine setting for Joomla 1.6 sites.
I've read through the documentation, troubleshooter and forum threads and I'm not sure whether this is a bug or if this feature isn't actually present.
The things I've done are as follows:-
I've downloaded Remote Control 4.0.3 today on Windows 7 Pro 64bit and it updated to 4.0.6 beta. I'm backing up a Joomla 1.6.0 site running Akeeba Backup Core 3.2.2 and I've set the Configuration Archiver engine to ZIP format. Site backs up and downloads - but as JPA file. I created a second profile and tried that, but got the same result. Running a backup direct from Joomla back-end works fine and get a zip file. I've tried RC 4.0.3 against a Joomla 1.5.21 site and I get a zip file, so seems specific to Joomla 1.6 sites.
Many thanks!