One common issue that arises is the Global filter applied in Deski. Sometime during conversion Report Conversion Tool is not able to correctly interpreted these filter and they are not applied in the report. When you convert any deski report at the end of the conversion RCT gives you the list of report and against them, it shows which all functionality was not able to migrate. You need can have a look at those as well for better understanding.
You can setup Auditing to track down the conversion:
BI 4 How To: Planning the Desktop Intelligence conversion to Web Intelligence
- Kuldeep