Event flow in ABAP is different when executed via SE80 vs. via TCODE

Hi,
We have many existing custom ABAP report pgms that have a custom transaction code that executes them.  Regardless of how the pgms are invoked, the event sequence in the pgm is INITIALIZATION, AT SELECTION-SCREEN, START-OF-SELECTION. etc. 
Now, when I create a new pgm with a transaction code to invoke it, the event sequence when executing the pgm via SE38 is as before (All 3 events above are triggered).  However when I invoke the pgm via the custom transaction code, only the event At SELECTION-SCREEN is executed.  (Not the INITIALIZATION or the START-OF-SELECTION events).
We have upgraded our SAP GUI from 6.4 to 7.1.   We are upgrading our system from 46.C to ECC6.  I get this error in ECC6 and also in the old system 46.C which is causing me to question whether the SAP Gui is involved.  We are using SAP GUI 7.1 in both the 46.C and ECC6 systems.
Any help will be appreciated!
Thanks,
Deb

Hi All,
Here is my ABAP Code.  I have put break points in the code so I can track the sequence.
REPORT ZDEBNEW .
data zdeb(2) type c.
tables kna1.
SELECTION-SCREEN BEGIN OF BLOCK A WITH FRAME TITLE TEXT-002.
SELECT-OPTIONS: I_KTOKD for KNA1-KTOKD.
SELECTION-SCREEN END OF BLOCK A.
INITIALIZATION.
  zdeb = '1'.   "break
  sy-subrc = sy-subrc.
PAI
AT SELECTION-SCREEN.
  zdeb = '2'.  "break
  sy-subrc = sy-subrc.
START-OF-SELECTION.
  zdeb = '3'.  "break
  sy-subrc = sy-subrc.
END-OF-SELECTION.
  zdeb = '4'.   "break
  sy-subrc = sy-subrc.
As for the type of transaction I am using...I created it via SE93 and specify SELECTION SCREEN 1000.  I classify it as a Professional User transaction.  One other thing I have noticed is that when I view the new pgm via SE80 I do not see Screen 1000 in the left navigation panel.  If I try to create such a screen in SE80, it says it already exists.  I can see Screen 1000 from tran SE51.  In one of the existing old pgms, I do see screen 1000 when I view SE80.
Thanks for the help and interest!!!

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