lsmeans not estimable, but lsmean differences are? [R for BE/BA]

Hi all,

I have a funny situation with one of my datasets:

In a semireplicated trial I am using the lsmeans package and syntax like
lnCI=confint(pairs(lsmeans(M, "Trt"), reverse =F), level=0.9) 

to extract CIs from my model M where treatment is coded as "Trt" having two levels and it works just fine.

However, if I do something like
lsmeans(M, "Trt") 

then I am getting "nonEst" of both rows in the column for the derived lsmeans.

So, R is telling me that it can derive a difference of lsmeans but it can't derive the lsmeans individually. I find this quite annoying, possibly hard to believe. On processing the same data with WNL, it (WNL) seems to be able to derive LSmeans, and it is getting the same difference in LSmeans as R.

Did anyone encounter this situation? I am quite baffled myself . Google isn't my friend. My own understanding of the LSmean derivation is a bit lacking, otherwise I'd much prefer to just write code myself and not rely on the package.

I really wish I could publish the dataset for someone to reproduce the situation, but I can't offer to do so at present.

Many thanks.

Pass or fail!
ElMaestro