SkyWatcher mounts do NOT execute a meridian flip immediately after culmination of an object. With both my HEQ5 and EQ6-R it can take up to 15 minutes after culmination before the flip happens. As far as I know (and I have searched a lot for this) this cannot be configured in the mount. The only thing to do is to be patient. I haven't tried the AAP yet with my SkyWatcher mounts so I don't know what the meridian flip behavior is but I would assume that the AAP keeps on trying until the flip succeeds. If this is not the case then this should be changed in the AAP.
EDIT: in case this isn't clear: all that AAP does is issue a GOTO. It is up to the mount to decide whether or not a meridian flip needs to be done. There is nothing that AAP can do about that so it is a mount issue (or rather feature).