Because everyone's timers are so inconsistant I'm definitely inclined to say "toss them in the trash bin".
http://pitoftheoni.blogspot.com
If this was 40k, or a tournament, or something Serious, I'd be inclined to agree.
But considering that this is just a light-hearted boardgame, does it really matter? If you toss out the timer, you don't get to use the cool timer, don't see the sand slipping away in front of your eyes.
When you factor in the fact that you're meant to both swap sides (so normally both use the same timer and have the same advantage/disadvantage), I see absolutely no reason to not carry on with the timers.
My roomate and I have played 2 games so far (Mission 1 then 2). He always plays the Space Marines and I the Genestealers. So far he has yet to run out of time, but I stress so far. I have seen the later missions and I suspect that some of them will involve the timer alot more.
We have also talked about not using the chips for the Command Points and rolling a D6 and agreed it was the same odds. We also agree that the Genestealer player not knowing the number of Command Points is really more important then one first thinks. As the Genestealer player there has definetly been a few times when I didn't take an action becuse I did not know how many points he had left. Admittedly I'm not a fan of the whole" after each round the Genestealer player needs to look at the Command chip to make sure the Space Marine player didn't cheat", but I really like whole "mystery" of the chips.
I have read other people on other forums even mention that they don't think the blips are important and they just play with Genestealers visable to both players. They still use the blips to find out how many Genestealers they get however.
"If you build a man a fire he will be warm for a night, but if you set a man on fire he will be warm for the rest of his life."
Imho by using a hidden Command Point system, you apply a slight amount of pressure on the Genestealers when it comes to weapon jam repairs. For example, if an opponent knew you have 6 CPs to spare, he will delay his advance for a turn, since you can potentially have up to 6 repairs. If he didn't know however, he might be tempted to try to rush a model, only to lose a model or two before realizing you might have 6 CPs to spare.
Of course, there's also the joy of scaring the Genestealer into thinking you might have 6, when you only have 1 CP. It's all about psychology
haha, mine jammed first time I tried to time it...............