I think you will find that this behaviour is by design.

The Resume Data that gets sent to the LMS is more relevant to the scored interactions such as quiz question slides. It's not (as far as I am aware) keeping track of every single slide the user visited.

Most LMSs, and most SCORM courses, are looking for some kind of a Pass/Fail score value.  Since you're actually using slide completion instead, you may find that the bookmarking functionality doesn't work quite the way you would like.  As a suggestion, try turning off Resume Data bookmarking (check the box for Never Send Resume Data) and check the option in TOC settings for Self-paced Learning.  Even this may not be enough to give you exactly the result you want because technically the SCORM is not supposed to be storing or persisting its own data.  That's what the LMS is supposed to do.

100% slide completion relies on each slide being played right to the end.  If you have click boxes or buttons on slides and any of these use an action that jumps to another slide, then the original slide (where it jumped from) will not have been played all the way to the end, and therefore you will NOT be able to get a 100% completion score.

Your options are:

• Set your navigation interactive objects to only use Continue.  However, this may not be possible if your course has any branching.
• Set your required completion percentage lower to allow for the slides that are not played all the way to the end.
• Use a widget like the TickTOC widget to artificially mark slides as completed even if they were not played all the way to the end.

I don't know of any way to make adjustments in Captivate to get the check marks in the TOC to persist from one session to the next. Once you have closed down the Captivate movie it does not store any data about all of the slides you visited. 

The Self-paced Learning option in TOC settings is only to bookmark the last slide the user visited and return them to that point on their next visit.  It does not check off all slides up to that point in the TOC. 

This is the way Captivate currently works by design.  The only way you might get around it would be to have a widget custom built to achieve your desired functionality. You'd need to engage the services of an ActionScript developer.  That would cost quite a bit of money.

Your LMS cannot change this behaviour, and neither can your client.

This is actually quite a complex issue. On the one hand you actually have two bookmarking methods to choose from. But on the other hand they don't play nicely together.  If you want to use bookmarking (so that the user can resume where they left off during a previous session) you have to choose between the built-in Self-Paced Learning option in TOC settings, and the Resume Data bookmarking found under Quiz Reporting settings. 

Self-paced Learning is designed for situations where you are NOT using an LMS, to allow the user to start again from the slide they last visited during a previous session.  It writes a small amount of data to a Shared Object (Flash Cookie) on the user's computer.  I've looked at the data in these cookies and they DO actually appear to record how many slides from the beginning of the movie you have completed.  And if you have Self-paced Learning turned on, your TOC can show previously visited slides as ticked on subsequent sessions. (I've verified this with a test project consisting of 5 slides.)  But there's a catch...

If you're using an LMS, having BOTH Self-paced Learning bookmarking AND Resume Data bookmarking turned on at the same time seems to result in issues where the bookmarking mechanisms within Captivate get into a bun fight trying to decide which one has right of way.  There have been a number of issues reported in these forums over the years that turned out to be due to bookmarking duels.  Self-paced Learning bookmarking is mainly interested in slide completions.  Resume Data bookmarking is more interested in tracking user interactions. It's looking at things that would be significant in the SCORM world, especially any scored objects or quiz questions.

So it seems you are forced to choose between one of the two bookmarking methods and neither one will give you everything you want.  Having Self-paced learning ON will tick TOC items on subsequent visits, but is not usually recognised by your LMS.  Resume Data bookmarking is designed for (and is actually part of) the SCORM standard, but is not recognised by the Captivate TOC.

So blame whoever you want for the way this all works (or fails to work as you would like,) however like many issues in life, it comes down to working out which is your higher priority.  As the wise pop musician once said: "You can't always get what you want..."