It is possible that the file that you are saving is fine, you are just loading it into Excel incorrectly (hard to know for sure without example). When you import into Excel there are ways to specify what the separator is and other options. You could also simplify the process by setting some options in write.table. Also check your regional settings, the default separator may be different depending on if your computer thinks it is in Europe (or certain countries) or the USA (or certain other countries), it could be that your version of R and your Version of excel don't agree on which region (and therefore which separator to use) you are in.
You may also want to look at the XLConnect package which will create excel files directly without needing to go through a text file. (there are a couple of other packages that will also write to excel files, but XLConnect is the one that I have had the best experience with).
Another option for quickly transferring a data frame or matrix to excel (at least on windows, not sure if this works on other OS's) is to use write table with file="clipboard" and sep="\t", then in the Excel window click on a cell, then do "Paste" and the data will be in excel via the clipboard rather than a file.
write. - Metricswrite.csv2? - Roland