Cubs are #10 in the NL in runs scored per game (#13 in total runs). But, Cubs are #5 in team OPS.
The only NL team who is as out of whack as the Cubs in runs scored/OPS are the Braves. They are the converse. Braves are #5 in runs scored but #10 in team OPS.
Not surprsiingly, Braves outperform their runs scored/OPs because they are #1 in team OPS with runners in scoring position. Cubs, on the other hand, are #15 in team OPS with runners in scoring position.
Diagnosis: a fluke.
I think there's more to it than that. I think Fukudome is such an outlier from the rest of the team in OBP that just the raw team numbers don't tell the whole story. Kosuke has a .468 OBP. Reed Johnson has a .444 OBP in very limited playing time, and Jeff Baker is at .364. No one else is better than .336. Outside Fukudome and Baker, there isn't a good OBP on this team among players who have had any kind of consistent playing time. And even Johnson and Baker are pretty much useless as OBP guys against RHP...on days a righty starts against the Cubs, Fukudome is the only guy who gets on base consistently.
The Cubs are currently 6th in the league with a .322 team OBP. But if you take Kosuke out, they drop all the way to .310, which would put them in an 11th place tie with Milwaukee, one point ahead of the 12th place Braves. That's a pretty severe drop based on just one player, especially when you consider he has missed out on ~40 PA due to platooning and his leg injury.
Just to provide a little more context, I looked at the Mets...they're 5th in OBP at .325, the closest score to the Cubs. They have 5 guys with at least 50 plate appearances who have a OBP higher than .336 (including 4 every day players: Beltran, Reyes, Davis, and Wright), plus 3 more with limited playing time who are above .336. If you take their best OBP guy out (Beltran, .383; with 37 more PA than Kosuke--so he should have a bigger influence on his team's stats), their OBP drops to .318. That would drop them all the way from 5th to a 7th place tie. Not nearly as severe a drop.
The bottom line is that the Cubs have been a bad on base team outside Fukudome. His high OBP may make them look superficially pretty good...but when 8 of the 9 players in your lineup have trouble getting on base, you're not going to score many runs no matter how often the 9th guy is getting on (especially when that 9th guy has gotten himself past first base only 3 times in his 45 times on base).
By the way, I wondered if Soriano had a similar influence on SLG because he's such an outlier...but he doesn't really because his low BA keeps his SLG from being as much of an outlier.