The agents are more to do with obscene wages/salaries rather than transfer fees. They do play a part however.
The problem I have with the transfer window system is that it encourages panic buying. You have a very limited time in which to purchase a player, and once the season is started, just four weeks. And panic buying, as we know, often results in simply throwing money at other clubs to sign a player hours or even minutes before the deadline.
Under the old system, the window was open during the season, and was closed a few weeks before the end of the season before reopening in the summer. Teams had the luxury of time to purchase players during the season; purchasing/loaning a striker with those extra goals if you were in a relegation fight or that confident centre back if you are in a relegation dogfight, for example. If your team was struggling, or just outside the promotion places in March, you were able to bring someone in. You can't do that now.
I can understand the problems with this, the old system and why they changed to the new system. The old system, because you could buy players at any time, concurrently meant that you could also sell players at the same time so many of the less affluent clubs had very much a revolving door policy.
But I think this new, shorter window with its panic buys has contributed to the increased transfer fees. The money itself has come from the wonders of satellite television and obscene sponsorship deals.
An off topic post, but football is football and not many people seem to debate it on this forum.