If you have
data[, 6] <- factor(data[, 6], levels=c(1,2,3,4,5),labels=c("very probable", " ", " ", " ", "very unprobable"))

in the data (adding a space for each label) : it fix the issue ?

(really time to move R and SPPS to seperate plugin …)

No, this would not fix the problem. As long as there are labels with the same value, R will treat them as equal. One way of fixing it, would be the following code:
data[, 6] <- factor(data[, 6], levels=c(1,2,3,4,5),labels=c("1 very probable", "2 ", "3 ", "4", "5 very unprobable"))
That way you would get unique labels and still keep all information from the questionaire.
Plano

Fix committed to master branch: http://bugs.limesurvey.org/plugin.php?page=Source/view&id=27434

@Plano : question about « No, this would not fix the problem. As long as there are labels with the same value, R will treat them as equal. One way of fixing it, would be the following code:»
If you have for label
'Great','Something','Great' : it broke too ?

Then we must ALWAYS add the code ? Right ?

Yes this would brake the code too. While I'm not sure how often this problem arrises, adding always the code seems a good idea.