I believe all people are saying is that having the bulk of a lineup as switch hitters makes you succeptable to certain pitchers and your numbers may be reflecting that.
Berkman is underperforming for you right now, but should pick up the pace. Frankly you won't get equal value by dropping him -- the players you list have some mashers in the bunch but Berkman should kill RHP and not do much against LHP (his obp is decent enough that you could use him).
Your park is a singles park, and will drag down bphrs period, but for Lefties and switch hitters vs. RHP.
If I made up your order I'd go:
1. Lofton DH L
2. Ianetta C R
3. Berkman 1B SL
4. Vlad RF R
5. Beltran CF SL
6. Huff 3B L
7. Figgins LF SL
8. Rollins SS SL
9. Roberts 2B SL
I don't think you need Duffy on the bench. You can pick up a .50 utility outfielder, drop Jenks and put the rest of the money into a mildly right balanced R2 with low WHIP and low natural HRs. Especially if you've decided Jones is your closer now.