Hello Sopan,
I just wanted to let you know I am having the exact same issue (using ArcGIS 10.1 and ArcSWAT 2012.10.1.13) when I get to this point in my project setup. At least one other person at my University also experiences the same issue.
Some findings:
I visited the ArcSWAT_WeatherDatabase in ...SWAT/ArcSWAT/Databases
PR_W1_1 is the name of a column in this database once you open one of the weather generators (I'm using WGEN_US_COOP_1980_2010). It follows PCPSKW12 and is followed by PR_W1_2.
From visiting the I/O documentation for CH12 (.wgn), I see that this skew coefficient is listed as PCPSKW(12) while our source of error is listed as PR_W(1,1). If you assume the parenthesis were not supposed to be there, you could change the column name in the database to PR_W11.
When I save these changes and attempt to use WGEN_US_COOP_1980_2010 in ArcSWAT setup, my error now reads:
The INSERT INTO statement contains the following unknown field name:
'PR_W1_2'. Make sure you have typed the name correctly, and try the
operation again.:IN, mWriteInputFiles.wgn
It seems PR_W11 is accepted as a valid header. The only thing I can come up with is that somehow the extra "_" is not supposed to be in the column header? However, I would caution that, from this change, the program could now be reading numbers in the column formerly marked PR_W1_1 (changed to PR_W11) as the wet day probabilities for November even though I think they were originally intended for January. Realistically, I don't think this is a valid "fix", but it is the only findings I've come up with after playing around with this problem.
Also, if I go back to previously created .mdb databases for other projects (which include a table called .wgn), there is a column there called PR_W1_1 so clearly this header name has not been an issue in the past. Hopefully others will chime in.