This can happen due to the fact that the Jetpack mod destroys and re-creates your character rather than move your character from the ground to the "jetpack" layer. It's like a Star Trek transporter - you're not actually moving but getting destroyed and re-created.
The destroy/recreate means I can't rely on item ID#s being unique so I do a much fuzzier match based on what information we do have - the armor's item name and grid contents. The downside to this means that if you and I are in the same game and we both have more or less identical armor (for example, an armor that's all jetpacks), there's a chance that the when jetpack re-creates the armor, SAS will think that you and I are wearing the same suit of armor and "helpfully" overwrite the intended color.
As a temporary workaround, if you and your multiplayer buddies make your equipment grids unique (say, one of you removes a jetpack and adds in night vision goggles in one corner, and the other does the same in a different corner) it should be enough to guarantee that your armors are treated as unique.
The Jetpack folks are going to fix the destroy/recreate thing in their next version so I haven't prioritized a fix for this. But, since it's clearly turning out to be an actual issue for folks, I'll go ahead and try to get that fixed today. If you can tell me exactly which version of the mod you've seen this in, it'd be a big help.