Sounds to me a bit like this boils down to the aforementioned issue between Leon, his agent and Wednesday....
The issue between between Leon, his agent and Wednesday is almost certainly regarding Leon's signing on fee/bonus.
The agents involvement will be that he is negotiating on Leon Clarke's behalf.
As I understand it, players when they sign a contract are given a signing on fee, a substantial part of which is deferred. If the player requests a transfer they lose their entitlement to this signing on fee. Sheff Wed don't want to have to be liable for this amount, particularly as it is bringing forward a payment that they probably wouldn't have to make for a couple of years but for the fact that he is leaving. Southend presumably don't want to pay it and are saying it wasn't part of the transfer fee that has been agreed so it is therefore an issue for Wednesday and Leon Clarke to resolve. Leon Clarke (or rather his agent) will be saying that he is contractually due this amount.
It will probably come down to who wants this move to happen the most: Wednesday to get him off the wage-bill, Southend to get him playing, or Leon because he wants to be at Southend.