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Thanks for your question.
I assume that you have now registered the permit. If you have then it should not affect your applying for a a new sponsored job.
It should not affect your application for ILR unless the UKBA attempts to hold that this failure speaks to a lack of good character, which in my view would be unwise since you could always appeal the decision on the basis that this was an honest mistake and you rectified the position within a reasonable time. Your application would have a fairer hearing on appeal in front of a judge who knows the law rather than an immigration official at the UKBA. If they accept that it was genuinely an honest mistake then your appeal would be allowed.
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I do not believe you completed that last post in its entirety.