Hi, when I am in the new Thanagar area, my CR gets boosted to 276 as it should, but, when i open a box from the missions and receive a new piece of gear, without looking too much at the IL gain, the stats say i get loads of red negative stats based on the boosted CR. So if i don't check the IL ill think its a massive descrease.
The stats on your current gear (stuff you're wearing) are being buffed essentially. Thus any new gear will appear with red stats because it's not being buffed. General rule of thumb for this circumstance: if the level of the new piece of gear is higher than what you wear, put it on to raise your CR.
That's why I warp to my base before opening any boxes. I see the true stats that way, and I have to go there anyway to update my armoury so I can sell the old gear.