Exactly as stated by HP and BritBrat, the two cables are probably just wired differently. Where did the two cables come from... I assume the RJ11-BT one is not the one that came with the phone?
It's also worth pointing out that the RJ11 'dsl' socket on most(/all?) microfilters isn't actually filtered at all, it just connects directly to the incoming line- pair. So I'd say the second microfilter is just acting as a wiring adaptor to give the required continuity to the phone. And since you have it daisy-chained off the phone-side of an earlier filter, you still get the required filtering that isolates the phone signals from the DSL so everything should probably work, if a little unconventional.
- 7LM