This problem may be related to this bug we just found in BPS/BPS Pro Network/Multisite htaccess writing code. This bug would impact all Network / Multisite subdomain site types and only Network/Multisite subdirectory GWIOD site types. GWIOD stands for “Giving WordPress It’s Own Directory”. This bug is being fixed and we will have new versions of BPS and BPS Pro released ASAP.
http://forum.ait-pro.com/forums/topic/maintenance-mode-frontend-only-syntax-error/#post-17182