SQL Server 2012 Replication - MSrepl_commands growing all set to in progress
So we're working now, I'm not 100% sure which part of this fixed the issue but I'm putting it down for if anyone else has this issue in the future where there doesn't seem a logical reason for the distribution growth.
Our distributor is on a windows failover cluster across two machines along with a Reporting Instance (and a MSDTC).

The issue occurred after a restart where the distributor moved from
server 2 to server 1 running along side reporting(and MSDTC).

After server 2 restart was complete Reporting was moved over to
Server 2.

This is when the issue was noticed.

The Distributor was moved over to Server 2 (Alongside reporting) but this seemed to have no beneficial effect

The Distributor was moved back to Server 1 and MSDTC was moved to server 2 with Reporting
At this point running the sp_MSdistribution_cleanup with a max time of just shy of how long the server had been running for (by 6 hours) and it cleared out everything (Took close to 3 hours to complete but it got there)