Why heat can not reverse my formaldehyde cross-linking product

I was trying to pull down some associated proteins with my bait protein by formaldehyde cross-linking. my bait protein is 3XFLAG-tagged. So my final step is to elute my proteins out by Low pH glycine. Then, the eluted protein was split into two samples. One is kept in ice after adding 2X Laemmli sample buffer, and the other is heated at 90 degree for 1 hour with sample buffer. Surprisingly, I found the cross-linking products were not revered by heating. Instead, heating produces many high molecular weight material stayed on the top of the gel. I don't understand what wrong with my experiment. Thank you for suggestion.