In my marathon game i just had, i allied with the thalan while playing Terran and the diplomacy grapth did not have the blue line connecting showing we were allied.The matrix grapth stayed showing the trading grath colour.The main relations UI page said i was allied, but in the UI section showing all the matrix style relations grapths it said we just on friendly terms.I saved and reloaded a couple of times and it stayed showing the wrong grapths.