R: trouble reading dates and time - r

Question

I have some problems in reading in date and time in a proper way, and I wonder why I get these problems. The problem is only on my windows installation of R. Running the exact same script on my UNIX installation works fine.
Basically, I want to read in a file with data and time as the second column, like this:
TrainData[[i]] = read.csv(TrainFiles[i],header=F, colClasses=c(NA,"POSIXct",rep(NA,8)))
colnames(TrainData[[i]])=c("comp","time","s1","s2","s3","s4","r1","r2","r3","r4")
However, only the dates are read, not the times, and my data looks like this:
comp time s1 s2 s3 s4 r1 r2 r3 r4
1 1 2009-08-18 711 630 69 600 689 20 40 1
2 5 2009-08-18 725 460 101 705 689 20 40 1
3 6 2009-08-18 711 505 69 678 689 20 40 1
4 1 2009-08-18 705 630 69 600 689 20 40 1
5 2 2009-08-18 734 516 101 671 689 20 40 1
6 3 2009-08-18 743 637 69 595 689 20 40 1
7 4 2009-08-18 730 577 101 633 689 20 40 1
8 2 2009-08-18 721 511 101 674 689 20 40 1
9 3 2009-08-18 747 563 101 642 689 20 40 1
10 4 2009-08-18 716 572 101 636 689 20 40 1
Running the exact same cond on UNIX returned both time and dates.
When I read in another file in the same script, with dates and times in the two first columns, I get the correct format of the date/time:
TrainData[[i]]=read.csv(TrainFiles[i],header=F, colClasses=c("POSIXct","POSIXct",NA))
colnames(TrainData[[i]])=c("start","end","fault")
returns
start end fault
1 2010-10-24 04:25:53 2010-10-24 11:22:33 6
2 2010-10-30 12:57:16 2010-11-02 12:29:54 6
3 2010-11-05 10:40:17 2010-11-05 11:59:51 6
4 2010-11-05 17:07:37 2010-11-06 14:30:01 6
5 2010-11-06 23:59:59 2010-11-07 00:14:49 6
6 2010-11-06 23:59:59 2010-11-07 00:14:49 6
7 2010-11-06 23:59:59 2010-11-07 00:14:49 6
8 2010-11-06 23:59:59 2010-11-07 00:14:49 6
9 2010-11-06 23:59:59 2010-11-07 00:14:50 6
10 2010-11-06 23:59:47 2010-11-07 00:14:51 6
Actually, I found a solution that works, eventually, but I wonder why I get these problems.
It appears that my Sys.timezone is set to "Europe/Berlin". If I set this to NA, the times will be read in as well, i.e. using Sys.setenv(tz=NA). If I then run the same code, my data looks like this:
comp time s1 s2 s3 s4 r1 r2 r3 r4
1 1 2009-08-18 18:12:00 711 630 69 600 689 20 40 1
2 5 2009-08-18 18:14:27 725 460 101 705 689 20 40 1
3 6 2009-08-18 18:14:31 711 505 69 678 689 20 40 1
4 1 2009-08-18 18:14:43 705 630 69 600 689 20 40 1
5 2 2009-08-18 18:14:47 734 516 101 671 689 20 40 1
6 3 2009-08-18 18:14:51 743 637 69 595 689 20 40 1
7 4 2009-08-18 18:15:00 730 577 101 633 689 20 40 1
8 2 2009-08-18 18:29:33 721 511 101 674 689 20 40 1
9 3 2009-08-18 18:29:37 747 563 101 642 689 20 40 1
10 4 2009-08-18 18:29:45 716 572 101 636 689 20 40 1
The other file still get times, but now consistently two hours different.
This is how the csv-files look like (basically, text separated by commas):
this is my file (basically text separated by commas):
1,2009-08-18 18:12:00,711,630,69,600,689,20,40,1
5,2009-08-18 8:14:27,725,460,101,705,689,20,40,1
6,2009-08-18 18:14:31,711,505,69,678,689,20,40,1
1,2009-08-18 18:14:43,705,630,69,600,689,20,40,1
2,2009-08-18 8:14:47,734,516,101,671,689,20,40,1
3,2009-08-18 18:14:51,743,637,69,595,689,20,40,1
4,2009-08-18 8:15:00,730,577,101,633,689,20,40,1
2,2009-08-18 8:29:33,721,511,101,674,689,20,40,1
3,2009-08-18 8:29:37,747,563,101,642,689,20,40,1
4,2009-08-18 8:29:45,716,572,101,636,689,20,40,1
Why am I having these problems with reading in the times? I would expect that it is not correct to use tz=NA, but this is the only way I found to work. Can anyone help me figure out why the times are ignored when tz = "Europe/Berlin"?
Is it generally adviced to put tz=NA when reading files like this? Even if this seems to work in reading in the times, the tz="NA" results in warning messages when I later want to work with the data:
Warning message:
In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'NA'
Can anyone help me explain the differences I get?