It depends. Transferring to other departments or positions within a company, across subsidiaries of the same company or going through multiple acquisitions is not considered job hopping. When managers are worried about job hopping, they're worried about the recruitment, training and opportunity costs that come with short-term stays in long-term positions. Most of that isn't an issue when you're transitioning into another role. In most cases such employees fill a much-needed gap elsewhere in the organisation or are better able to grow and thus more motivated. All of this are things they encourage.
What can be a black mark is when the positions you held have no logical connection. Going from software programmer to an admin role to accountant is generally not something you want on your resume as it demonstrates a lack of dedication and bad judgement on part of the candidate. Going from programmer to consultant to project manager is a much more logical transition. Any transition that indicates an increased responsibility is
unequivocally a good sign.
As for your resume, you'll want to group all your positions under a single company and indicate the subsidiary or branch alongside the role. Try to show a logical progression in responsibility but don't lie.
Whether you bring this up in your cover letter depends on the positions you held, your experience and the type of job that you're applying for. The fact that your company wanted to keep you on even when their employees don't normally make that kind of transition also speaks well of your work ethic. If you can word it well, that's something you could actually use to sell yourself in an interview. Nick Young's comment is an example of that, though I wouldn't bring up the reasons behind the transitions.