Well that could be it… first of all I assume you mean ‘company’ A and B, and A has a subcontract or similar relationship with company B, and they are the ones authorized to put you in or otherwise “turn on” the eQIP. Nobody can open up an investigation on you without a reason so it could be that the one company is waiting for the other.
And things get gummed up from time to time as well, regardless of company issues. But what you need to be aware of is that somewhere a clock is ticking, and just because you didn’t get the link in time doesnt mean the clock stops ticking. So make sure you have all the necessary info and get right on it when they do allow you to log on to the eQIP site.