The Carrier gas flow rate is 3ml/min (Nitrogen). Most things I have read suggests a slightly higher than normal flow rate for this sort of analysis.
OK, I would agree with that.
With the column at 50C there is a danger that water will condense in the column, which will distort the peaks and probably damage the stationary phase.
What concentration of analytes do you have in the samples ? If the concentration is high enough you could try a split injection, which makes the water matrix a lot more tractable. Trouble is that Uniliners with the hole at the top do not owrk well with splitting.
This is a resurrected thread started off by someone else - can you summarize your problem and set up so that everyone is sure what it is that we are talking about.
Peter