This has been pretty confusing because the common perception is that after 6 weeks a player is eligible to come off the PUP list within the three weeks that follow.  This is true, but often misread.  Here is how it should be phrased:

Once the mandatory 6 week period of PUP status to start the season has expired, a team then has a 3 week window to allow that player to start practicing.  Once the player does start practicing, a separate 3 week clock begins on the player in which the team has to decide whether to activate him to the 53 man roster or place him on IR and end his season.

The Colts actually give us a perfect example of the complete rule this season.  After 6 weeks Tyjaun Hagler began practicing immediately.  From the day of his first practice, the Colts would have had 3 weeks to active or IR him.  They deemed him ready right away and activated him (he took the roster spot vacated when the McCargo trade fell through and he was sent back to Buffalo - essentially LuJaun Ramsey's roster spot).

This brings us to Ryan Lilja.  Wednesday marked 3 weeks since he was eligtible to come off the PUP list. So the Colts HAD to allow him to start practicing or IR him.  This was the latest possible date they could start the 3 week "do or die" clock on his status.  They NOW have 3 weeks to decide his fate.  He DOES NOT take up a spot on the 53 man roster, so no one will have to be cut to make room for him.

It's very confusing because the rule widely reads as if the whole process takes 9 weeks max (6 on PUP and then 3 to practice and make a decision).  The real rule, however,, is that it can be UP TO a 12 week process (6 on PUP, up to 3 to either IR the payer or begin his practice "clock", and then the subsequent 3 week "clock" that Lilja is now mandated to be on).

Hop all this helps clear things up.