Try to get an overview of what is wrong in the file. This also sheds some light on the competences of the people making these files. The files have seemingly undergone manual editing without taking care of the correct number of columns. The following perl code lists the lines which do not have 14 items:

 cat 014850_D_AA_20070207.txt | perl -naF"\t" -e '$i++; s/\t/<tab>/g; print $c++." : line $i has ". scalar @F ." entries \n$_\n" if  @F != 14' | less

With the following result:

[...]    
559 : line 40908 has 2 entries 
A_24_P937084<tab>A_24_P937084

560 : line 40936 has 12 entries 
A_24_P938135<tab>Z25424<tab><tab>Z25424<tab>Hs.515032<tab><tab><tab><tab><tab><tab><tab>H.sapiens protein-serine/threonine kinase gene, complete CDS. [Z25424]

Now, you could complain to Agilent that for the money you pay them, they should provide you with correct files, or repair yourself, trusting them that the files do not contain more errors.

You can make a file with all correct lines like so:

 cat 014850_D_AA_20070207.txt | perl -naF"\t" -e"print if  @F == 14" > ok.txt

And one with the rest accordingly:

 cat 014850_D_AA_20070207.txt | perl -naF"\t" -e"print if  @F < 14" > notok.txt

and rescue information in excel manually.

The result ok.txt still contains ' - default quote character for read.table - like in 3'-UTR and # - default comment char - (exon # 5), so in order to read all columns into R, you should use the following settings:

Update:

any.biological.annotation = read.table("ok.txt", sep="\t", quote="", comment.char="", na.strings="", header=TRUE)

This might be a good preset for parsing most biological annotations in R. Never use the fill=T option (unless you are prepared to shoot yourself in the foot), because that will just cause errors to go unnoticed.

I received an answer from Agilent when I emailed them:

Gene Name or Gene Symbol is not always available for all our probes, but the other columns in the file you sent are also annotations : accession numbers (from GeneBank, Ensembl, etc…) and description.
Some customers make the mistake of thinking that every transcript has its own GeneName or GeneSymbol, which is just not true. Also keep in mind that this Rat design was created in 2007, so some the probes that were selected back then based on public databases have since then been deemed inappropriate, or classified in most recent databases as irrelevant, etc… This explains the "unknown" status most of the time I believe. Even if we annotate probes regularly, we never take un-annotated probes out of a design, so if such a probe is in a given design, it just gets a different annotation in the next round, but it stays on the design. If customers want a more recent design, they should look into design ID 028282 or 028279." The arrays are often designed before all the genes are known for an organism. This can for example be done using sequencing data from mRNA samples, as you see for several probes on the rat array you use. Later versions of the design will have better and better annotations, as progress is made in the research community. For the version you work with, 22.884 probes has been assigned a genename (this is all the genenames that has been available from GeneBankl, Ensembl etc). How you choose to use the data from the rest of the probes is really up to you. By far most of the probes has the accession numbers from GeneBank etc listed, even if the genename is unknown. One way of annotating is then to use the accession number instead of the genename for those probes. The probes labeled just "unknown"/no info, I would probably skip in further analysis.