LLVM 3.4 performance regressed?

Question

I use the Spec 2006 benchmarks to measure the performance of a few private passes and the generated code. So far, all my work was based on LLVM 3.1.

Last week I wanted to move forward with LLVM, and I rebased all of my passes to LLVM 3.4. This required only adjusting a few #include lines. However, after that change I measured a huge performance regression. Next I disabled all of my custom passes, but still performance was down. Here are the numbers of a few Spec benchmarks compiled with LLVM 3.1 and 3.4

            LLVM 3.1  LLVM 3.4
            --------  --------
401.bzip2       7.50     17.5
429.mcf         4.72      8.10
456.hmmer       4.18     10.1
458.sjeng       4.85      8.86
433.milc       13.4      26.0
470.lbm        13.4      12.6

I also noticed that the number of functions called by e.g. 456.hmmer went from 6 to 45009; similar numbers show for most other benchmarks. Inlining failed?

I compile the Spec benchmarks with

CC=clang -g -std=c89 -D_GNU_SOURCE -c -emit-llvm

and then call opt with

opt -simplifycfg -mem2reg -break-constgeps <my-passes> benchmark.bc -o benchmark.schnufte.bc

Once opt is done, the bitcode is lowered with llc and linked into an executable.

The performance regression is very noticable, and I doubt that 3.4 would have been released with a regression as obvious as that. So my question is: did I miss something? Are optimizations now invoked more explicitly? I added -std-compile-opts to my opt call after my passes, but that didn't help at all.

EDIT As suggested, I posed the question to the LLVMdev mailing list, but the thread receives little attention.