Not sure if these discussion boards are the best place to get help (the majority of the users are going to be UK radio folk)
The SDI fibre extenders shouldn't be an issue - just like ethernet to fibre media converters they are just passing the raw ones and zero data via light rather than electronically.
You don't state which exact Blackmagic boxes you are using, if you are coming in or out as analog connections somewhere there is every chance for a level mismatch. The blackmagic boxes have balanced audio in/outs - (i.e. nominally +4dB level) if you are feeding this into an unbalanced audio input (nominally -10dB level) you'll have every chance of distortion as you're feeding too much signal.
Some of the Blackmagic converters have a computer utility you can use to adjust settings, so you may be able to change the in and or out levels to match the application.
If you give us some details of the kit you're feeding into and out of the link we might be able to advise more.
Myriad user since 1998, now custodian of dozens of Myriad,Autotrack, Powerlog and Scoop boxes of many different flavours.