Traditionally, these committees were supposed to be nonpartisan. The notion was that the conference committees ought to honor the spirit of the political compromises that had been made during the debates over the legislation in each chamber. Obviously this was a crucial procedural job, but given that the goal was essentially to find common ground, it was ultimately a rather boring bureaucratic function.(For more on this procedural issue, check out this useful C-Span site.)
Over the last couple of Congressional sessions, however, this formerly boring function has changed quite dramatically. While it might be excessive to say that reconciliation committeework now reeks of derring-do, it has certainly become a less purely bureaucratic function. Since the Republicans took control of both chambers, these conference committees have become a place where the goal is not to split the difference between Senate and Congressional versions of bills, but rather to continue the partisan battle under nonpartisan, bureaucratic cover. On numerous occasions, Republicans have used the "reconciliation" process to purge bills of language or clauses that were inserted to help bring centrists and Democrats on board with the initial vote.
The goal in this transformation of the conference committess has been very calculatedly political. Centrists and Democrats have repeatedly been faced with the very uncomfortable prospect of having to "vote against a bill after they voted for it." For the Republican congressional leadership, the goal has been to try to expose these centrist legislators to charges of "flip-flopping." What's worse, with Republicans commanding very strictly voting discipline from their rank and file, they've often they've been able to simply forsake the Democratic votes during the votes on reconciled bills. The political goal in these cases has often to get a few Democrats to vote for the first version of a bill (thus providing political cover for Republicans against charges of partisanship), then to create a much more partisan "reconciled" version of the bill that passes along a strict party-line vote.
The result of the Republicans' habit of amending bills in conference in this manner, of course, is that it has made it all but impossible for Democrats to consider seriously making any kind of compromise on important issues. Any time Democrats agree to any legislative compromises, they now know they run a significant risk that the Republicans will drop their own concessions in conference. In short, the habit of amending bills in conference has led to the not unfair impression that the Republicans essentially bargain with the Democrats in bad faith.
For a very insightful take on how this may play in the struggle over Social Security, check out this fine piece of political reasoning from Matt Yglesias:
You reap what you sow.
Some dastardly Democrat is contemplating a deal with Lindsey Graham wherein "current payroll tax revenues are left in place for now and private accounts are funded in whole or in part from new payroll tax revenues generated by raising or even lifting the payroll tax cap." This is a moderately bad idea on policy terms, and a simply terrible political idea.
Most crucially, the House Republican leadership has already ruled it out. Thus, the only possible effect of brokering a compromise of this sort with moderate Senate Republicans would be to create a conference committee in which whatever concessions the GOP makes to turncoat Democrats will be purged from the bill. Then, having already conceded the high ground on the need to "do something" and on the point that the "something" ought to involve private accounts, turncoat Democrats will be forced to argue that the only problem with the conference report on the phase-out is that it doesn't raise taxes. This will, at best, transform a political winner for the Democrats into a political loser and, at worst, lead to the passage of a bad phase-out bill.