Defence in depth ..
I had exactly the same situation in the game I started yesterday, took 3 planets in line, dressed for defence, before I was able to stop the waves. Taking on 2 8.6 Vicious Raiders I got 3+k Raiders (mk2) and 2 regular (mk1!!) waves (one had 2.2k frigates), which all hit in seconds of each other (well, the raid engines triggered before, but they didn't cross over untill the other waves hit).
Still being at 6-7 planets and mk1 waves it took me 3 times a full fleet to defeat them, more or less a rebuild fleet per planet ... and 3* a full cap of mk1 FFs.
Costly, but it pretty much opened up the map for me ... 1 hour in.
Edit: Should also mention that the game loved trowing Neinzul Roaming Enclaves at me during the above ordeal, painfull. (When do I learn that nasty AIs dont combine well with Roaming Enclaves/Hybrids?
)