write.table: strange output has been produced

Good afternoon all -

While making a steady progress in learning R after Matlab I encountered
a problem which seems to require some extra help to move over.
Basically I want to merge a data from biological statistical dataset
with annotation data extracted from another dataset using an 'id'
crossreference and write it to report file. The first part goes
absolutely fine, I have merged both data into data.frame but when I try
to write it to csv file using 'write.table' it seems like it does write
the 'data.frame' object but it also insert some parts from the
annotation data which are not suppose to be there...
There is a little snapshot of the file output below to illustrate. The
upper half is fine, that's how it should be. The lower half, which is
actually appears to be space-separated, not coma, obviously grabbed from
the annotation dataset and is not supposed to be here.

--------------------------------8<--------------------------------------------
"344","166128",126.44286392082,179.904700814932,72.9810270267088,0.40566492535281,-1.3016395254146,2.47449355237252e-07,4.2901159299567e-06,"Chitinas
"18816","238247",92.5282508325735,135.981255262454,49.0752464026927,0.36089714209487,-1.47034037615176,2.5330054329543e-07,4.38862252337004e-06,"Prot
"22072","222365",30.8191942806426,52.4262903365628,9.21209822472236,0.17571524068522,-2.50868876576414,2.54433836512085e-07,4.40531098485028e-06,NA,N
"25062","226605",30.808007579908,50.3976662241578,11.2183489356581,0.22259659575825,-2.16749656564076,2.54934711860645e-07,4.41103467375713e-06,NA,NA
"7539","247009",75.4175439970731,34.4643221134552,116.370765880691,3.37655751642533,1.75555313265164,2.60010673210741e-07,4.49585878338091e-06,NA,NA,
"407","267139",425.559675915702,279.393013150954,571.72633868045,2.04631580522577,1.03302881149302,2.61074218843609e-07,4.51123710239304e-06,NA,NA,NA
"26530","171300",146.80096060985,80.0063286553601,213.595592564339,2.66973370924738,1.4166958484644,2.68061220749976e-07,4.62888115991058e-06,NA,NA,N
"3078","159013",34.3260176515511,52.4580790080106,16.1939562950917,0.308702808057816,-1.69570948866688,2.69104298652827e-07,4.64379716436078e-06,"40S
"4657","159998",133.10761487064,185.450704462326,80.7645252789532,0.435504009074069,-1.19924209513405,2.75544399955331e-07,4.75176501174632e-06,"IMP-

171597  171597  KOG1347 Uncharacterized membrane protein, predicted
efflux pump General function prediction only    POORLY CHARACTERIZED
171658  171658  KOG4290 Predicted membrane protein  Function unknown
POORLY CHARACTERIZED
171660  171660  KOG0903 Phosphatidylinositol 4-kinase, involved in
intracellular trafficking and secretion  Signal transduction mechanisms
CELLULAR
171660  171660  KOG0903 Phosphatidylinositol 4-kinase, involved in
intracellular trafficking and secretion  Intracellular trafficking,
secretion, and
171703  171703  KOG2674 Cysteine protease required for autophagy -
Apg4p/Aut2p  Cytoskeleton    CELLULAR PROCESSES AND SIGNALING
171703  171703  KOG2674 Cysteine protease required for autophagy -
Apg4p/Aut2p  Intracellular trafficking, secretion, and vesicular
transport   CELLU
and metabolism     METABOLISM
--------------------------------8<--------------------------------------------
And this is a piece of code that produced this:

--------------------------------8<--------------------------------------------

n = nrow(statdata)
extra = data.frame(kogdefline=rep(NA,n), kogClass = rep(NA,n), kogGroup

= rep(NA,n))

subset = intersect(statdata$id, annot$id)
MR = match(subset, annot$id)
ML = match(subset, statdata$id)

extra[ML,1] = as.character(annot[MR,2])
extra[ML,2] = as.character(annot[MR,3])
extra[ML,3] = as.character(annot[MR,4])

# strangely, if I do
# extra[ML,] = as.character(annot[MR,2:4])
# it produces digits (???) instead of a string value

mergedData = data.frame(statdata, extra)
write.table(mergedData, 'filename.csv', sep=',')

--------------------------------8<--------------------------------------------

Any ideas why this is happening?

Many thanks
-Igor