My colleague has been doing the CSR generation in both, because we have cases where we need to install the same cert in two different IIs/ISA, and it doesn't work if he doesn't do this.

Any idea what could cause this?

I intend on using openssl as I'm used to to generate those keys/CSRs, any pitfalls?

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If you need the same cert on both devices, why are you doing two CSRs? Two CSRs will result in two different certs. – Shane Madden Nov 18 '11 at 18:00
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