On July 2, 2006, an auxiliary engine room fire broke out on the Columbia temporarily impairing steering and propulsion on her northbound voyage from Bellingham in Seymour Narrows in Canadian waters.

She motored to Duncan Bay, British Columbia for damage assessment before continuing on to Ketchikan's Alaska Ship & Dry Dock for more extensive repairs.

Early on 15 August 2007, only two months before a scheduled overhaul, position number two connecting rod in the Columbia's starboard engine experienced a bearing failure.

Soon it became apparent that she would require further work, and in a controversial decision the Marine Highway System chose to cancel all further summer voyages on the ship pending repairs.

The repair of damage sustained to the port main engine viscous damper drive coupling during the middle of the 2009 operating season was remediated as well.