I suspect there is a problem with your configuration file, this would give the problem you describe. To test this your would rename the existing file and allow the Moneydance to create a new one. The file is called config.dict.
If you're using a Mac, it should be located at one of these locations within your Home folder:
If you have any trouble finding your Home Library folder you can open Finder and hold down the option key while selecting the Go menu and the Library folder option should occur or you can open Finder and select Go -> Go to Folder and copy and paste in the following:
This should pull up your local Library folder.
If you're using Windows, it should be located under your login directory at:
C:\Documents and Settings\(yourusername)\.moneydance\config.dict
Depending on your version of Windows
If you're using Linux it should be located in your home folder at:
Once you've found your config.dict file, ensure Moneydance is closed and rename the file (to something like config-org.dict, for example), then open Moneydance again and it will appear as though you've just installed Moneydance for the first time and may have to locate and open your data set again.
Now try the operation(s) you were having trouble with and see if it works as expected.
If it does you can continue using the new configuration file by while viewing your data file, choose Help --> Register Moneydance and input your license key.
If you run into any problems, you can simply close Moneydance and rename config-org.dict file back to config.dict and open Moneydance again to restore your original settings.