They still haven't gotten this fixed in 2012. What about 2013?
I am just deleting the station reference from the structure label rather than mess with this. I have even individually changed the alignment setting on a structure, later edit the strucuture, and have the alignment setting vanish, especially with data shortcuts.
This is especially aggrevating when creating aligments from pipe networks. The network is created first with no alignment set for the network. The alignment setting is added later, when the alignment is created, but it won't 'take' and the station labels keep showing as blank.
I have an easy solution"
Add to your Structure Profile Label a Reference Text component that references an alignment station. When you place the labels, you will be prompted to pick the alignment. Pick the other one than the one the pipe network references. You are able to have stationing from both alignments represented.
The example is not refined, but it shows that this can be done.
Delta Engineering Systems
Autodesk Authorized Value-Added Reseller
If you are talking strictly profile views, the answer is simple: instead of having your profile view label address the alignment that the structure is associated with, use instead the alignment that the profile view is associated with.
To accomplish this, in the profile view label use an alignment reference text for stationing. When you select the structure in profile view to label, it asks you which alignment you want to use for the stationing. Right click, a list of all available alignments appears, then select the alignment associated with that profile view. The correct stationing appears and all is well.
Note that in profile view you can only station reference one alignment per structure automatically. In other words, you cannot have a label that says "STA. 10+00 ROAD A = STA. 14+25 ROAD B" without hand editing, a very bad idea.