More often than not, when things run really slow, it's because code is being fetched out of external. Any PC address above 0x000xxxxx is going to slow things down by >100X.
Can you try this just to make sure all the critical code is running out of local?
1.) e-ojdump -D "your_epiphany.elf" > dump (tar and attach)
2.) e-run --trace "your_epiphany.elf" > trace (tar and attach)
Thanks,
Andreas