One likely point of conflict: the consumer financial protection agency. The House bill calls for a standalone agency, while Dodd has housed his in the Federal Reserve. Senate Republicans, though, want to rein in the scope of its rule-making authority, and give it the power to pre-empt stronger state laws. The White House and most Democrats are strongly opposed, but if the GOP prevails that could cause a bit of a dustup when the House and Senate bills are merged.
This tells you all you need to know about the conservative tissue-thin commitment to states' rights. Republicans don't control the White House. They don't control the House. They don't control the Senate. But in this instance they would like for the federal government to preempt state and local laws governing the financial sector, on the off chance that some progressive state legislature somewhere tries to restrict mortgage activity or payday lending or credit card rates or what have you.