Quartus 4.2 (full) vs Quartus 7.1 (web edition)

If the design is growing by 50%, then it's usually something you can observe. Open both designs and right-click-> Customize the hierarchy display so that each LCs/Registers/Memories/DSPs/etc. are displayed(basically as much info as you can get). Then compare how big each hierarchy is below the top-level. Most likely there will be one culprit that is 3K LCs larger. Expand that hierarchy in both designs and repeat at that level, working your way down until you find the offending hierarchy. My guess is that it will be something like a RAM that uses memory but in 4.2 uses registers, or something like that. But hopefully it is fixable.

The other possibility, which I believe is less likely to occur, but is much harder to debug, is if every hierarchy is "a little bigger". That might mean in the 7.1 design something gets reduced that then trickles through and reduces logic in a number of other hierarchies. But taking a design from 11K to 8K LCs is pretty drastic, and should be somewhat noticeable as to what's occuring.

Note that it's worthwhile to have the latest version though. Technicallly, you could probably target a Cyclone III device and get similar performance at a much better price point.