This is more a comment in case anyone else runs into this issue - I'm using Gviz to plot output from RepeatMasker, and the column of TE names is "Target" in the .gff - when plotting with Gviz, the transcriptAnnotation input would just place the text "unknown" with this command:

te_grtrack <- GeneRegionTrack(gff, name="TEs", transcriptAnnotation = "Target")

plotTracks(list(te_gtrack, te_grtrack))

transcriptAnnotation also seemed unwilling to accept any other column - so I renamed the "Target" column to "symbol", and that worked perfectly. I'm just getting started and I'm not sure exactly why that is, but I figured I would make a note of it - is there something obvious that I am missing that would allow me to plot without changing the column name? 

this is what worked:

colnames(gff)[9] <- "symbol"

te_grtrack <- GeneRegionTrack(gff, name="TEs", transcriptAnnotation = "symbol")

plotTracks(list(te_gtrack, te_grtrack))

GeneRegionTrack objects are not simple wrappers around GRanges objects, but instead impose a certain structure like gene identifiers, transcript identifiers and human readable gene symbols. Thus it expects the input data to populate these required properties. Your repeat masker data is not really gene model information which is the main design idea behind GeneRegionTrack, so I'd suggest to use AnnotationTrack objects instead, which is a bit more flexible.

Florian