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Let's face it -- Ks are the number one item that attracts pundits and fans to pitchers.  NOBODY gets thrilled about watching guys like Washburn or Wang or Lowe work.  Even when they have non-K methods of getting outs beyond the normal "random" BABIP, the fans largely don't care - and the bulk of the math says they should be ignored, too.
But, the thing that REALLY pumps FIP (or any of the other 'true' ERA methods) is HOME RUN RATE.  When Olson and Vargas were winning ugly early, I was one of the lone Olson supporters --- but with the codicile that he HAD to get his HR rate down.  It went up (2.3/9) ... which happened to French (2.0/9) ... and Morrow (1.8/9) ... and Fister (1.7/9) ... and Vargas ... (1.6/9) ... and Jaku (1.5/9). 
In point of fact, RRS is the only non-ace sporting a reasonable HR/9 rate (1.0). 
The club doesn't play at Coors field or Arlington.  There's NO blaming these numbers on the park.  When one guy comes in and has a dinger problem, you blame him.  When you get two, you blame one and chalk the other up as bad luck.  When you get a HALF DOZEN guys all showing the same problem, then your problem almost HAS to be at a higher level.
Early in the season, there was a massive split in dingers surrendered between Joh and Johnson.  After Joh's return, Johnson was catching the "good" pitchers, and Joh the "bad" ones, so it gets a LOT more complex figuring out if Joh is really the problem or not.  But, at this point, IMO, the HR problem *HAS* to be blamed on "something" beyond the individual pitchers.
Possibilities:  Johjima  (always has carried a horrid comparitive CERA and opponent OPS compared to his teammates.  In 2009, this manifested early as a massive HR difference, which has shrunk a bit as the year has gone on -- and Johnson has seen his PT significantly cut).  The .779 to .665 OPS is driven by an 80 point slugging differential.
Coaching/Strategy:  The veteran pitchers (and Felix), have had success this season in keeping the dinger totals down.  The HR barrage has been specifically limited to the long line of young guns, (except RRS).  Snell, who has pitched miserably in terms of K-rate, BB-rate, and has an absolutely dreadful K/BB ratio, is next up with a liveable 1.3/9 rate.  Perhaps what the club is TEACHING the young guys is a mitigating factor that "might" be artificially inflating their HR rates.
Player selection:  The dinger-fest is also largely focused on Z acquisitions.  Olson, Vargas, French and Snell had no contact with Seattle coaching until they arrived.  Olson only had 1.1 and 1.2 HR rates before arriving.  But, in addition to the 4 imports, you've got Fister and Jaku and Morrow as home grown HR explosions. 
My suspicion?  I think the club likely has a very good aggregate plan that could possibly keep the HR totals down.  They just don't have guys talented enough to execute that plan w/o making too many mistakes.  ANY of them could grow out of that with continued work, as they're all so relatively new to the bigs.  I also think Johjima likely exacerbates the situation. 
My recommendation?  I think the club desperately needs to trade Johjima, (even if he isn't the problem), because I don't think it will be possible to figure out what the core problem is while he remains.  I think the club needs to SERIOUSLY reassess its game planning with its young pitchers.  I have a sneaky suspicion that they may have OVER-stated (to themselves), the ability for Safeco to suppress HRs.  It helps "some", yes.  75 to 87 HRs as I write this.  But, not as much as hoped for ... AND it's likely teaching bad habits to the young guys.  Maybe the young guys can eventually learn to adapt to home/road changes in game planning.  But, for 2009, the 0.38 ERA edge at home seems more about the 45 hit difference, and not the 12 HR difference. 
In any case, one of the top priorities for 2010 will be locating the root cause of the problem, whether it is catcher, coaching or Z ... and fix it.  Because, the club at this point is looking at having Felix and 4 prayers for a rotation.  Hopefully RRS continues impressing.  But, if the Seattle staff does its best to surrender gophers as if they played 1/2 their games in Arlington, the club can kiss any hope of leading the league in ERA buh-bye REAL fast.