Hi and thank you for your post.
You are using real time continuous mode which relies on the PC or OS to dictate the timing and hence you will not be guaranteed to get 1ms/S due to overheads within the operating system. Since you are using the 3424 you can use streaming mode, where this time you are not restricted by the OS overheads and since the scope has its own memory and clock you will get your desired times.
The number of samples is limited to 1,000,000 per channel in one PLW file, if you have more samples it will create another PLW file automatically with a number denoted at the end. So if you wish to view the information at a later date you would load more then one PLW file.
Hope this answers your questions.