Can't say I have the exact same issue however I can link BUT I can't do anything with the link because in Pokemon Emerald (only tried this one so far) it won't save properly, I've used the auto detect for save size/type and manually on Flash 64/128k both just say
"Save failed. Checking the backup memory... please wait. Time Required: about 1 minute"
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I have tried isolating this VBA-M version, .gba and .sgm files (this includes allowing it to reset and create a new config file and not having any .sav files) so it seems to have an issue with creating the .sav.
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For the time being I have reverted to the 1229 build (in which linking doesn't work) Any help or suggestions would be greatly appreciated!