I'm seeing this too. I am on the test server so I don't know if that makes a difference or not. Additionally it would appear to ignore some characters that are on the CT altogether. I can't reproduce this consistently. I'll do some more testing.
Edit: Ok did some more testing. new Campaign, imported a couple of PCs and added them to the CT. The extension didn't register their presence on the CT in any way. Added in an encounter from SKT. and the NPCs were added to the CT but without any hp or attacks etc. I gave the two NPCs different dice (one a d4 and the other a d8) and then rolled initiative. Both NPCs rolled 16 which is clearly wrong. Of course I may well be misunderstanding how this works but I assume that initiative is rolled in the normal way from the Menu on the CT. I couldn't find any other way to roll the initiative. When I joined my own game I could then select the two PCs and give them dice but I couldn't find a way to roll their initiative from the player side. As it happened the NPCs rolled low and went 1st and second but then when I moved the CT on after the second NPC it jumped to the PC with the highest roll missing out the PC with the lowest roll. It then jumped to the 1st PC with the lowest roll. I suspect that the test version has changed something which may well be causing these issues.