Hello @sandip2,
What I meant with the second questions was: Are you using the same QSPI Flash IC part number as the eval board? the eval bboard uses the following:

If you are using the same flash, you should change the algorithm in your flash tool as the following:

Please note that the QSPI number and CS may differ depending on your design.
You mentioned that your board works correctly in debug mode, are you changing the BOOTMOD pins to boot in serial mode? you should use the following configuration [S32E27XEVBUG, Rev. 1 — 31 August 2023, page 4]:

the pins in the S32E chip are [S32E2_IOMUX.xlsx, attached with the S32E2 reference manual, sheet S32E2_IOMUX, rows from 105 to 119]:

About the pins you mentioned (AC31 and AC32) I think there may be a little confusion, I checked the functionality of those pins and they are not QSPI related, I meant to which pins are you connecting your QSPI Flash memory and I don't see QSPI functionality in those pins, moreover, one is an RCON bit [S32E2_IOMUX.xlsx, attached with the S32E2 reference manual, sheet S32E2_IOMUX, rows from 1353 to 1363]::

Let me know if I correctly understood the information you shared.