So shaking it down will get it partially compact but it really does need a little more, I've found a measuring cup, I'll have to double check the size in the morning, works REALLY well to squeeze everything in tightly once it's about 3/4s full. Any bit of space between the resin spheres can cause a decrease in efficiency.
Can I ask what you're currently using to measure TDS? Is it a standard dual meter? Your high initial TDS is probably related to a phenomenon know as TDS creep. This is when you start producing product water initially and the first 30 seconds to a minute of water has extremely high TDS coming out of the membrane from previously accumulated particles that have come loose out of the membrane. This will always happen when you start your production up and it's usually advisable to add a T valve to your setup on the product water line after the membrane and before the DI resin. This way you can direct the super high TDS from the initial product water down the drain with the "waste" and once the product water gets within range of the membranes proper rejection rate you can turn the valve and direct the much lower TDS water towards the DI resin. This can vastly increase the life of your resin over the long term.