Hi there sparklyscott, we had a problem with cheques in our business bank, a short explanation of the Business Banking Code to their counter assistant followed by a visit from their Area Manager soon got our cheque clearance times down to 2 days for ANY cheque.
The thing to point out to them is that if they vary terms and conditions of your account, you must be informed in writing within a certain period (forgive me for not having the exact amount of days to hand, it is either 14 or 30 though). They cannot decide on a individual cheque by cheque basis what will clear faster and what will be slower (unless they suspect you of money laundering that is!), and must give you a maximum period of time for cheques to clear, for instance 5 days, so that if you do your accounting around the maximum figure, you should be fine.
What prompted my complaint to the bank was the fact that a teller who processed one of my larger cheques had forgotten to do it, until the next day, so to cut a long story short the bank wanted to add another day onto clearance because of their error. When I first complained they tried to explain clearance to me, but quickly changed the subject when I let them know I am an ex-banking advisor and perfectly aware that even a clearance cycle of 5 days is over long. As mentioned above, I showed them in their copy of the Business Banking Code where they could not just extend my clearance times, asked them if I was suspected of fraud or money laundering (a great question, if they answer yes and I am a fraudster, then they go to jail also for tipping me off!), needless to say I withdrew the required monies that day, and now after speaking to the area manager (as mentioned above), cheque clearance times are 2 days, and have been for around 12 months.
If in doubt, rip somebody a shiny new one.