House Speaker Mike Johnson and Senate Majority Leader John Thune are openly clashing over Homeland Security funding, complicating Republicans' path out of the 72-day shutdown.Why it matters: Thune is unlikely to say it publicly, but frustration is running high among Senate Republicans over Johnson's failure to pass a DHS appropriations bill that cleared the Senate — twice.The two leaders began the month with a joint statement and a joint plan of action: fund ICE and Border Patrol through reconciliation, and the rest of DHS through the regular appropriations process.DHS has warned that its stopgap fund to pay staff will run out in the coming weeks. Driving the news: Johnson (R-La.) is looking to modify the Senate-passed DHS bill to secure votes in the House. As written, it doesn't have the votes to pass until after a reconciliation bill is passed."It has some problematic language because it was haphazardly drafted," Johnson said of the bill funding the non-immigration parts of DHS."We have a modified version that I think is going to be much better for both chambers. It doesn't change most of the substance,' he said.Moment laters, and a few hundred feet away, Thune (R-S.D.) was asked to respond. He was diplomatic, but his message was clear:"I think we did everything we can to ensure that everything is appropriately funded," he said.Later, Thune seemed open to working with Johnson on how to alter the bill."We're working with the House to see if there's a way to do that," Thune said.Zoom in: The main point of contention in the House is around language that "zeroes out" funding for ICE and Border Patrol in the Senate-passed appropriations bill.A wide group of members want to strip that language from the Senate bill, avoiding taking a vote seen as defunding law enforcement.They're still considering waiting for the reconciliation process to be complete, and pairing a final vote on that with the DHS appropriations bill. But that would likely leave the department shutdown through mid-May.Between the lines: Johnson appears to be signaling relatively minor edits — more of a stylistic rewrite than a substantive overhaul.Even small changes would require the Senate to take up and pass the bill again.The bottom line: Both men are Republicans. Both are leaders. And both are staking out public positions that could make a private deal harder to reach.