Happy to help and offer advice. I would be very concerned about not recording full hours onto the company time card system. A few reasons for this are that HR should run checks on their staff on a regular basis to ensure working time regs are being taken into consideration. Of course businesses generally need staff to do more hours than the working time regs allow for and I don't believe you are saying you won't but at the same time any decent HR professional should be reviewing staff hours and where there are excessive hours should be writing to/contacting the staff to discuss the issues.
Also, the majority of companies that undertake redunancy programmes tend to use utilisation as one of their scoring mechanisms. Especially if they have a time card system. Utilisation has good and bad points but if you are being asked to record your actual hours elsewhere and HR aren't aware of this then if your business was to undertake a rationalisation process you may score badly in this area due to your time cards not being correct. Of course you would be able to raise this at your briefing session and obviously this is not the case for you at present but who knows what is around the corner. If I found out that I had undertaken a process based on system information that was being manipulated I would be furious as it would make me look like I didn't know what was happening in the company and also the plonker who did it never came clean and would undoubtedly know about the process we were undertaking as it would be announced throughout the business and as a manager he/she would probably have some input into the initial scoring anyway. Bluntly, if he worked in my company and did that his life would not be worth living.
Two final points about time cards are, companies implement these systems for various reasons. One of the main ones being it allows Finance to project profits and I'm assuming Finance use your current time card system to do that. Mind you if you have to fill in a differnt sheet for client charge outs maybe they don't and then what is the point of a time card system other than to check up on employees and ensure they are doing the hours they should be which you could have any decent manager do anyway.
In terms of work-life balance documents you need to approach someone in HR to find out what their true view on that is. Nearly every company will espouse it as a policy but very few actively encourage and support it. You need to understand whether it is a mission of your companies to achieve a better work-life balance or are they just paying lip service to staff and IIP or other accreditations. The only time things like this work is if they are supported by the MD and filtered down through the organisation.
All in all, if you approached me on a confidential basis about these issues I would ensure no one knew it was you who raised these issues but I would ensure that the issue was dealt with and resolved. I don't know your HR team but would believe they would treat this in the same way.
Do you have any relationship with anyone in HR at all? Can you have a friendly chat over a coffee or even just pop into their office quickly? Do you need to go to HR or can you raise this with your boss. I am very concerned at him manipulating the system. It doesn't surprise me as it happens all the time but when I find things like this out where I work I'm like a dog with a bone as I know people don't hide things unless they are doing something they shouldn't be.
Ask your boss (innocently) why you should not record your full hours on the time card system. Don't let him give you an answer full of waffle. A little bit of pressure to put him on the spot won't hurt him. I appreciate you need to be aware of your relationship with him so may not want to do this.
Final long waffly answer for you is, if HR aren't doing their job properly then someone needs to give them a kick up the butt. They have a responsibility to the company but also to the staff. It would be very unusual for them to be audited on their hours in terms of working time regs but at the same time they have a duty of care to their staff. In fact if you use the words "duty of care" when talking to HR this generally puts the frighteners up them. Most forget it but it's always part of their remit and when courts hear they have failed at this - big trouble. Hope this helps.
In a nutshell (boy do I go on) I don't think you should be doing what your boss wants, I have serious concerns and think someone needs to be aware of it. If they do nothing about it then that is their responsibility but at least someone has been notified.