It seems to me that your earlier reply (which explained that it was not you that had travelled on that day) has not been linked to the prosecution file against you.
I urge you to reply again, but this time you are going to have to do a bit more work to avoid a prosecution. . . .
First, reply again to the Company, enclosing a copy of their letter to you, and a copy of your earlier letter, and clearly repeating that it was not you, and that any attempt to pursue you in the Court will be defended.
Because there are now three parties involved in this (you, the Company and the Court) all correspondence should be copied to all parties. So, secondly, reply to the Court's SJP notice indicating that you will plea 'not guilty', and include a copy of your letter to the Company (plus the copies you enclose with it).
If you don't do all of the above, there is a high probability tht this will drag on for longer than it need do, or that you will be sentenced under the SJP by default.
I also urge you to contact the Company's prosecutions team by phone again, to make sure that they understand that your response to their investigation is that it was not you who travelled, and that they should link your reply which explained that, to the file they have against you. You should avoid explaining whatever evidence you have of what you were doing that day which demonstrates that it wasn't you, but do let them know that if they wanted to proceed with a prosecution, then you would put them to proof (to demonstrate beyond all reasonable doubt that it was you that travelled - it would be at that stage, if it gets that far, that you would be able to introduce your evidence of where you were at that time).
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bf3ftw, if you don't put in the time to do as I've suggested, and instead, if you follow this line of reasoning, then you will probably find yourself in Court quite swiftly:-
Whilst I agree in principal that it wasn't a good idea to ignore this surely the onus shouldn't be on the OP to do something or it lands up in court?
The SJP is a default system, set up to deal swiftly with offenders who do not 'do something' in reponse and/or who do not present a defence. If you adopt Antman's approach then you will find it hard to avoid it 'landing up in court'. It's already well on the way to being dealt with by a Court!