I couldn't answer on why all clients are disconnected without seeing your programming, but I can tell you that there is no way around the MAC ACL for specific SSID(s). It is true that the MAC ACL applies to the entire radio. You could however, have the dedicate a radio to SSID(s) that you do no want to filter. It is probably not practical or efficient, but that would technically work.
The only way I know to filter by MAC for specified SSID with Adtran products is to go Bluesocket with vWLAN. It works great.
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Thanks Noor, it turns out there was a bug in the software that was not allowing the MAC Access list to work properly. The load I'm using today is NV1638A-R10-4-0 and I have no further issues. This addresses the MAC access list, and not the feature request of being able to apply a MAC access-list per SSID. That still requires a separate radio.