Hi Sten,
I am assuming that you are using the latest development version of the package since you are already setting the transcriptAnnotation parameter (hint: always include the output of sessionInfo() when asking for help). With this I tried to simplify the setting of labels for GeneRegionTracks, and the idea is quite trivial:
rather than having to play with showId and geneSymbols, you can now set everything with just one parameter, transcriptAnnotation. It can take one of the values "symbol", "transcript" or "gene", and will use the respective annotation for the labels. If not set at all , or if set to "none", no labels are printed. You may wan to create your GeneRegionTrack like this:
grtrack <- GeneRegionTrack(ensemblData, chromosome=12, name="Transcripts", transcriptAnnotation="transcript", background.title="#40464C", cex.group=0.7, cex.title=0.8, fill="salmon")
plotTracks(grtrack)

Check out how setting the transcriptAnnotation parameter has an effect on your plot:
plotTracks(grtrack, transcriptAnnotation="symbol")
plotTracks(grtrack, transcriptAnnotation="gene")

I will try to make this a bit clearer in the vignette. Btw, there are several other ways to create a GeneRegionTrack, also from Ensembl data. You may want to consult the vignette. Most of those assume that you want to fetch data for a particular genomic region, so I am not sure whether those make sense in your case.
Florian

From: Sten Ilmjärv <sten.ilmjarv@gmail.com<mailto:sten.ilmjarv@gmail.com>>
Date: Tuesday, January 28, 2014 11:00 AM
To: Florian Hahne <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>>
Subject: Gviz pacakge

plotTracks(list(itrack,gtrack,grtrack), from = min(ensemblData$start) - 20000, to = max(ensemblData$end) + 20000)

	[[alternative HTML version deleted]]

