The first thing is to dig into your soil and see what you have. The only reason any plants roots would rot would be because the soil they are planted in is constantly too wet, a drainage issue. Contact the local office of your Washington State University USDA Cooperative Extension service about having a good, reliable soil test done so you know what your soils pH and nutrient levels are, then dig in with these simple soil tests,
1) Structure. From that soil sample put enough of the rest to make a 4 inch level in a clear 1 quart jar, with a tight fitting lid. Fill that jar with water and replace the lid, tightly. Shake the jar vigorously and then let it stand for 24 hours. Your soil will settle out according to soil particle size and weight. A good loam will have about 1-3/4 inch (about 45%) of sand on the bottom. about 1 inch (about 25%) of silt next, about 1 inch (25%) of clay above that, and about 1/4 inch (about 5%) of organic matter on the top.

2) Drainage. Dig a hole 1 foot square and 1 foot deep and fill that with water. After that water drains away refill the hole with more water and time how long it takes that to drain away. Anything less than 2 hours and your soil drains too quickly and needs more organic matter to slow that drainage down. Anything over 6 hours and the soil drains too slowly and needs lots of organic matter to speed it up.

3) Tilth. Take a handful of your slightly damp soil and squeeze it tightly. When the pressure is released the soil should hold together in that clump, but when poked with a finger that clump should fall apart.

4) Smell. What does your soil smell like? A pleasant, rich earthy odor? Putrid, offensive, repugnant odor? The more organic matter in your soil the more active the soil bacteria will be and the nicer you soil will smell.

5) Life. How many earthworms per shovel full were there? 5 or more indicates a pretty healthy soil. Fewer than 5, according to the Natural Resources Conservation Service, indicates a soil that is not healthy.
to see what else you need to do to make that soil into a good healthy soil that will grow strong and healthy plants.

Here is a link that might be useful: WSU CES

Thanks so much! I'll definitely try these things. At least I can say that it's a pleasant smell and I did see good number of worms, so maybe I'm headed in a good direction. I tend to think drainage is the culprit, as the former owner seems to have felt that bark/additional dirt needed to be added each year. The beds are over full, and we're actually lowering the level of each, so we can work on the drainage.

If the bed level is above the surrounding grade, that's good for drainage. In fact, it's about all you can do to improve drainage. Improving the soil in the hole or bed does not actually improve drainage, which is limited by the subsoil conditions at whatever depth it underlies the prepared soil. In periods of heavy rain, the hole fills up with water and the prepared soil will be saturated.