The thing to remember about the neck is that it's made of wood, which is a natural product where it's reaction to the environment is not totally predictable. This was true when Alembic built your basses and continues to be true in your environment as well.
The common practice in making guitar necks is that you assemble the neck, then shape and level the fingerboard and then the fret tops so that they're dead flat when the instrument is unstrung. When you string the bass to pitch, this will pull the neck into a bowed shape, then you adjust the truss rod to counteract most of that bow. If everything works out right, then the relief should be just right to prevent buzzes and give you can adjust the action to fit your playing style. Everything working out alright includes having the wood deform evenly along it's length and making sure you've properly designed the truss rod to provide support where your neck needs it.
On top of all this, wood may respond to humidity and temperature in ways that may change how it behaves - it may become stiffer or more flexy, or might do either irregularly along it's length. Over time, it may gradually change as a result of aging, too.
When your instrument was made, the setup was done by a highly skilled luthier (probably James for many of us!). They can do a perfect leveling of the fingerboard and frets, but they are doing this in the environment of the shop. There's no way that they can anticipate what the climate or conditions will be like when it gets to you and no way to tell the wood not to be reactive.
If you had two basses, never had troubles, then both basses developed the same action problems at the same time, then I'd guess the climate is a factor - probably that it's been drier or hotter than in the past. If the weather changes (with the seasons or if this has been an unusual year), then you may see the problem disappear on it's own. Or if this is the effect of aging or an ongoing change in your environment, then perhaps you'll need to have some work done. You could send it back to Alembic, but you risk facing the same problem - they can make it perfect, even to your hands in Santa Rosa, but it might not be right when you take it home. So, if this is a persistent problem, you may want to see if you can find a local tech who can work on this. If you're seeing this problem, then others may be seeing it as well.
I don't think this is likely to be an issue of quality control, because the quality that changed is probably your environment, not the instrument.
Now, you do bring up a very good point- why is this happening on my Alembic when it's not happening on a $500 Fender or Ibanez? Part of it may be that the wood just wasn't as sensitive to humidity changes. Every piece of wood really is different, whether it is going into a $500 or $5000 bass. You may find cheap basses that aren't affected and other ones that have much more change, or some other Alembic that isn't affected.
One thing that may also be a factor is that different instruments may have a wider range of truss rod adjustment. Having a wider range of truss rod effect may help improve the yield of sellable necks for a big builder. But in your Alembic you've paid a lot of money for fine tonewoods, and I think it's good design if the trussrods aren't intended to carry the bulk of the neck tension - that's your sound, you know!
For those of you that are familiar with Modulus instruments, the original design is an all-graphite monocoque (hollow tube) with no truss rod, and no way to adjust action other than through (expensive) fretwork. This wasn't an error in the design, it was quite intentional on the part of the company founder, Geoff Gould. He really believed in the audio benefits of having graphite bear all the structural tension and didn't want to dilute that with a truss rod. In later years, Modulus has come to adopt a truss rod for fine tuning playing action, although the adjustment range is limited because of the strength of the neck. Alembic necks are generally quite strong and stiff because of the laminated construction, so I think you may be seeing a little less adjustment range there as well.
There are dual action truss rods out there, but you should be able to get good results with either type. The tension of the strings always makes the neck bow, and the truss rod counteracts that. In a normal truss rod, the threaded adjuster that you turn is pushing against a block of metal attached to the neck. If you had a double action truss rod, it actually traps this block of metal on both sides, so loosening the nut actively decompresses the rod. But the tension from the strings is higher than the truss rod nut anyway, so loosening the truss rod should cause more bow in any case. All that the dual action rod buys you is that you won't loosen the adjuster off the threaded end of the rod. This is kind of like the way tuners work - a double action truss rod could push the action slightly higher, but it probably won't hold this position if the strings aren't providing the bow, just as your tuning won't be right if you tune down to pitch.
Sorry for the long rant. I'm not sure where you are, but it's hard not to notice this thread popped up again when the Midwest and East Coast of the US are getting a record baking (I did see that this thread started months ago though).
If this isn't the result of today's weather, it may be time for a visit to the shop. After 20 years, it would only be surprising if the wood characteristics HADN'T changed at least a little. When you read about a Stradivarius violin, it's not unusual to see what appears to be major surgery over the years. Of course, you want to maintain such a rare instrument in as original a form as possible, but it's also recognized that this sort of work is expected on any instrument.
David Fung