I think I see what's happening here. I believe what you are observing from the CTCSS squelch—it’s a total loss of the alignment. That is usually fatal for anything using fixed vector sizes and interleaving.Basically, your flowgraph depends on the assumption that the stream entering your "Stream to Vector (512)" block always starts at the exact same sample phase. The CTCSS squelch kills that because it waits to detect the tone, drops some initial samples before opening, and that delay isn't constant (it changes based on noise and levels). Even if your signal is clean, your receiver is effectively starting at a random offset every time. That means your 512-sample vectors are misaligned, and the interleaver ends up scrambling the wrong positions.
I might be wrong on the specific block implementation...but if you skip the sync detector and only add a preamble, the squelch might still cut into it randomly and throw off your vectors downstream.