The Quake 3 writeup cites exactly this problem as the reason Carmack abandoned the reliable+unreliable combination:

"His next iteration involved using UDP with both reliable and unreliable data, pretty much what many would consider a standard networking architecture. However standard mixed reliabled/unreliable implementations tend to generate very hard to find bugs, e.g. sequencing errors where guaranteed messages referenced entities altered through unreliable messages."

(from http://fabiensanglard.net/quake3/The%20Quake3%20Networking%2... )