When changing fiscal year, there will always be a "short year" that needs to be manually closed out in DBA because the system will not know there is a new FY date.  At the end of the short year and prior to processing anything dated in the new first full year using the new FY date, you need to do the following:  
   
1.  Go to AD-A and change the Fiscal Year Date to what it would be on the new calendar.  Ignore the warning message about not changing it here; this is the exception to the rule.  For example, if the FY is changing from May 1 to January 1 and the "short year" is 5/1/03 thru 12/31/03, then on December 31, 2003 use AD-A to change the FY start date back to 1/1/2003  
2.  Run AM-B.  This program assumes a full year but since you faked it out by changing the date in AD-A, it will post the YE entries as of the correct ("short") year end and reset the new fiscal year.  
   
If you are already into the new year and never closed out the "short year", then you will realize you are in trouble midway into the first full new fiscal year when DBA thinks it is fiscal year end according to the old date.  In that case, use AD-A to reset the FY date to what it should be (January 1, 2004 in the above example), then UT-K-D entering the correct dates allowing for the short year already past, then GLEREDO also entering the dates to correctly define the short year.

The instructions have changed.  Since the 2/07 update, the fiscal periods are defined in AM-N so you can define your short year accordingly.  Go into AM-N and edit the current year and repeat 12/1/08 as the start date for the last 4 periods.  Then set 1/1/09 as the "Next Fiscal Start Date".  If you are on something 2/7 or later but not the current version (as you are, Laura), you may not have the "Next Fiscal Start Date" on your AM-N screen and if you are going to have a short year, I recommend you update so that you can define it.

12/1/08 is the period START date for the last (and all remaining unused) periods.

AM-N (on the second screen) requires you to enter the starting date for each month, not just the year.  That is what I am referring to.

You need to first go to AM-N and leave all the prior years alone.  For the current year (your short year) the start date stays at 4/1/08, period 2 is 5/1/08; 3 is 6/1/08; 4 is 7/1/08; 5 is 8/1/08; 6 is 9/1/08; 7 is 10/1/08; 8 is 11/1/08 and 9 through 12 are all 12/1/08.  Then set the Next Fiscal Year Start Date to 1/1/09.
 
THEN after all the dates are set in AM-N you can run AM-B