yes, it will weak your case if you have presented the cheque in the bank before the receipt of the email confirmation. however, if you have compiled with the condition written on the back of the cheque, meaning thereby if you have banked the cheque after receipt of email confirmation from the vp of the company, it will make your case a strong one.
There may be points in your favour which will depend upon the facts and circumstances of your case. Please consult a nearest lawyer.
Written on the bank? Signed. If you don't have email facility, do you have to create it? How can such preposterous condition can be created? Tomorrow the drawer will write: Payee to come to his house with sweets to get confirmation.