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With both enabled, only the Clock bit gets set (2X mode) and and device has to be set into ISP mode again
to program the P89VRD2 again to set the security bit.

This is true for all the versions I have used so far.

Well it may hold for other members of LPC9XX family but I will talk for LPC936.

As per data sheet there are 8 nos 2K sectors. Each sector has 3 security bits assigned to it.
As per Flashmagic there are 32 Blocks. Each Block has 3 security bits assigned to it.

1) How do I interpret? Are security bits assigned to 2K sectors OR 512Byte Blocks (Mathematics says 4 blocks per sector).
2) Will I be able to use sectorerase and reprogram if I set the bit 1s of Blocks?

Sorry if I have missed in the datasheet or User Manual. 

Well, I use address 3000H for this (>1FFFH), write 01H and the 00H to FCF (0B1H) to get into boot code, call PGM_MTP (1FF0H) with right parameters, exit by writing 01H to FCF to get back to user code.

Nothing happens when I run. The bits do not get set and the micro resets.

Since it takes 2 steps to program the security and clock bit by flashmagic (security bit does not set if clock bit programed in same programed cycle), I had tried this.
Boot loader version is 7. FM version 4.60 (reason of not using 5.61 given in previous post).

Why IAP does not work to program these bits?

Setting the serial number in this version does not work. The verification can be done ( after power on/off).

Worse, once serial number is set by this version, setting of serial number in older
versions also does not work. You can read signature, security and flash (verify).
No message to use password.

My experiments have cost me the only 5 nos. P89V51RD2 left with me.
Some have boot-loader version 6 and some 7.

It was stupid of me to download this 2 days back and update. Fortunately I had an older version (4.60)
setup file somewhere in one machine.

That works, but not after the serial number set by 5.61.

This is a matter of serious concern.

Sorry if I could not make out, but I just want to program these using Flashmagic.

Other than connecting Tx/Rx/Vcc/Gnd (No feed for reset), what pin(s) should be pulled LOW for
getting into ISP mode on power-up ?

dpt

1) My way of getting into ISP mode is to give a command, normally "read signature" and then to power up, before OR after I get the "Reset the Device for ISP mode" message. Sometimes it takes quite a few attempts whatever method I use. That is not much I am worried about.

2) When I program with "Set Security Bit" and " Program Clock Bit" checked, the device programs but I get a message something like " Program Clock Bit" failed. I have to switch-off and power-up again to get into ISP mode and I see the Clock Bit set but Security Unset. I program again and and the security bit also gets set.

Now I have to program twice if I have to program both the 'Security Bit' and the "Clock Bit" (for X2 clock).

3) I am not too sure but if I set the serial password and then reprogram, the password does not work. Now I set the password after I program.
Can we not have a checkbox to set the serial password after the program sequence ?

When I program 89V51RD2 with Set Security Bit 1 and Prog Clocks bits enabled,
two things happen -

1) I get message that Clock bits could not be programmed. But a read shows that it is.
2) The security bit is unset. I then reprogram without ERASE . Now I do not get any
messages and the security bit too gets set.
This is dangerous as after programming with the parameters enabled, one assumes that
security bit is set.

I am programming new device without any erase at 57600 baudrate.

I have tried with latest version too, in fact today, same thing happens.

I never had any problem with the old RD2 or with P89C61X2BN, but here I am unable to
access the device by ISP (yes I keep PSEN low at time of reset) once I program the
device, security bit set or not.

No problems with P89C61X2.