I have the following code:

fit <- lmFit(intmat , designMatrix)

tmpfit <- fit[,-1]

lmfit.cont <- contrasts.fit(fit[,-1], cont[-1,2])

lmfitebayes <- eBayes(lmfit.cont)​

topTable(lmfitebayes, coef=name, number=Inf)

Which fails when executing topTable sometimes. Thats because contrast.fit in some cases prefers not to give a name to the coefficients (see below). It does not give the name if only a single contrast is being computed. If I than want to execute topTable and specify the name of the contrast "A - B" although usually it works.  Still, it would be nice to have the name because: being explicit somehow is more explicit than implicit, and being consistent is more consistent compared to having names once and not having them other times. 

> head(lmfit.cont$coefficients)
                 [,1]
A0A075B6P5 -0.6597603
A0A075B6S5 -0.3231210
A0A087WSY6 -0.1133279
A0A0B4J1V0 -0.1568641
A0A0B4J1V6  0.3889539
A0A0B4J2D9 -1.6330590

Reading ?contrasts.fit should tell you that the contrast matrix should be... a matrix. cont[-1,2] is a vector, which means that the column names are dropped; so any names you have in your original contrast matrix are lost. This may be contributing to your errors, though it's hard to tell because you don't provide an actual reproducible example that other people can run. For example, the code below works well for me:

# setup
intMat <- matrix(rnorm(6000), ncol=6)
groups <- rep(LETTERS[1:3], each=2)
designMatrix <- model.matrix(~0 + groups)
cont <- cbind(AvsB=c(1,-1,0), BvsC=c(0,1,-1))

# limma
library(limma)
fit <- lmFit(intMat, designMatrix)
lmfit.cont <- contrasts.fit(fit[,-1], cont[-1,2,drop=FALSE])
lmfitebayes <- eBayes(lmfit.cont)
topTable(lmfitebayes, coef="BvsC", number=Inf)