Hi there,
Well that is interesting! That .htaccess we have doesn't actually do much, it just prevents access to the readme.txt and screenshots so I may consider moving or modifying it. I don't know why this would fix your issue though, if you could check the apache logfile on the next update and let me know if you see anything when you try to save, that would be helpful.
Thanks for the feedback.
Regards,
Mark.