Did you read:
MAX PATCHES on Tommy14's excellent Error Resource Site?
Of course you did... After all, everyone talks about Tommy's.
So you will have tried -sparse in your hlrad compile won't you?
You will have increased your -chop value to under 96?
And you will have most certainly had a very serious look at the way your map is light, dynamically and statically keeping a close eye on textured lighting and the scale of large faces?
So since it isn't any of those potential problems, maybe someone can come up with another suggestion.