How frequently a train will be run through the train wash depends on whether the train will end up at a depot with a wash plant, and how intensively the train is used.
This would explain why FGW's fleet of 158s appears to be dirtier than SWT's fleet (the vinyl transfers on FGW's fleet don't help too since, as other posters have suggested, dirt becomes engrained more easily in vinyl). IIRC, most of SWT's 158/159 fleet returns to Salisbury, with only a few stationed elsewhere overnight, meaning the fleet goes through the trainwash at Salisbury on a more regular basis. Compare this with FGW's fleet of 158s, which are used more intensively and therefore can't use the trainwash at St Phillip's Marsh that frequently.
To the best of my knowledge, XC (pre Operation Princess), Central Trains, and Connex South East were known for the unkempt condition of their fleet, so lack of cleanliness is not a new issue.