I got a distress call to "Defend Settlement X". Fast traveled there and it was being attacked by a squad of Synths.

Since I'm currently on good terms with the Institute and actively doing quests for them, why are their Synths attacking my settlements?

One of the patch 'fixes' was to keep this from happening to The Castle if you were in the Institute, but I guess they didn't let that apply to other settlements also.

How far along are you in the MQ. Have you 'picked' the institute or are you just doing quests for them. Heck when I was for the RR I had to do so many Institute quests (by their request) that I about forget what side I was on.

I only started getting Institute attacks on my Settlements once I met Father (and started doing missions for him), they only ended when the Institute was finally dealt with......one plus is that the attacking Synths don't target you while trying to massacre your settlers while your on good terms with the Institute.

I wonder why they patched it for the Castle but not for the other settlements....

Oh Bethesda. You so silly.

Oddly enough I've never had any Synths zap in myself. I always just have the random settler get found out as a Synth, he gets killed, and then thats it.

I am doing quests for the Institute but I am not fully committed to them in the main quest.

The Synths were hostile to my settlers but not to me.

These were Gen 1's and 2's. At least five of them.