Hi John,
"Some questions: what is it in the log files did you see that prompted you to think BS1 was a virtual server? "
- Just an idea from this comparison:
SP9 1st WHEN no DESTINATION_APP test ran in 5 seconds
SP13 1st WHEN no DESTINATION_APP test ran in 317 seconds
Something is wrong with database access! It's a terrible difference on a VERY small scope!
"which OSS note or other documentation told you that they changed the *ELSE processing priority in SP13"
Not sure they post a separate note 
they think - no difference! And you don't need to change code, all *IS and *ELSE will be processed anyway!
Extra things: when I look on the simple code with no DESTINATION_APP I can see the following timing:
SP09:
COSTCENTER.PROG_ID <>""
QUERY TIME : 644.43 ms. 0 RECORDS QUERIED OUT.
CALCULATION TIME IN TOTAL :165.82 ms.
ELSE
QUERY TIME : 2677.06 ms. 12 RECORDS QUERIED OUT.
CALCULATION TIME IN TOTAL :890.86 ms.
WRITING TIME :493.90 ms.
Total sum of time: 4892 ms
SCRIPT RUNNING TIME IN TOTAL:5.14 s. - Reasonable (+250 ms for script processing and log writing)
SP13
COSTCENTER.PROG_ID <>""
QUERY TIME : ? ms. 0 RECORDS QUERIED OUT.
CALCULATION TIME IN TOTAL :? ms.
ELSE
QUERY TIME : 314.00 ms. 12 RECORDS QUERIED OUT.
CALCULATION TIME IN TOTAL :1.00 ms.
WRITING TIME :1.00 ms.
Total sum of time: 316 ms + some time to select and calculate zero records
SCRIPT RUNNING TIME IN TOTAL:317.00 s. - ???????????
Vadim