With woody shrubs there really isn't a way other than replanting them. I think you're right about why this is happening: it's combination of compaction as the air related fluff settles out, as well as decomposition of the organic matter that was in the original mix.

I assume you're going to be adding compost to the soil annually to keep the organic matter content up, and you might consider adding some mineral soil as well, or the triple mix you mentioned if one of its components is soil. Compost will pretty much decay away, but soil will not.

By adding some material you can at least reduce the sinking in the rest of the garden, and even around the shrubs if you're careful, but don't bury the stems of the shrubs. If they are going to be big ones, their own root balls will expand a bit as they grow, and that will help.

It's best to keep foot traffic off of clay, avoid digging when it's wet, and keep it mulched to retain moisture and prevent pounding rain from compacting the surface.

Thanks for the quick reply! To avoid the garden beds being trampled on (these ones surround my patio) I will actually raise them slightly and put a low wall around them. An extra 8 inches off the ground should help my back too.

The triple mix is a combination of soil, compost, and peat. In the future if I keep getting sinkage I guess I will try to add mostly soil. I have been using compost as mulch and I plan to till it in (where I can) come springtime and then top it with more compost. Hopefully that will keep the organic matter levels high enough.

When you prepared those beds did you till them?
Tilling soil introduces air into the soil mix and as that soil then settles and the air dissipates the soil level will fall, shrink. That is one reason why most sources suggest waiting a week or so after tilling, and wetting that soil as well, before planting.

Yes, I planted pretty much right away after turning up the soil and mixing in the amendments.

Actually, this leads me to another question: I have a ton (perhaps literally) of soil/clay that I am sifting to remove rocks, weeds, etc (the result of sod removal and stupid contractors who dumped gravel into the dirt pile!) The end product is a pretty fluffy material where the soil/clay is more like very small, uncompacted balls. I am putting these back onto new garden bed areas and then mixing in some compost. How long do I need to wait before planting in this sort of soil? Again I worry about the soil compacting and shrinking, but I also worry that there is no real structure to the soil.

Some areas will be planted next spring so no worries there, but other areas are places where I am raising the garden bed and so I need to re-plant my shrubs.

Thanks!

Soils with a lot of entrained air can appear to be nice and fluffy until that air dissipates. Adding adequate amounts of organic matter can help keep that soil nice and fluffy by keeping the clay particles apart. You want between 6 and 8 percent organic matter, humus, in that soil.