The company should be helping you with any potential visa switch. One of the questions you might want to ask them is how well versed they are with dealing with that. If they have a competent HR department that is used to helping new starters get the correct visa and work permit, then that would be a plus. Presumably there will be a process, like a number of meetings with them rather than one interview then 'ok you start on Monday' so I would try to schedule one of those meetings/interviews with the relevant HR staff there so that they can talk you through the process.
You will be asked for proof that you are in Malaysia during the application. If you are in Thailand, you won't be able to provide that and your application will be denied.
You've been in Thailand for 120 days, there's no 'fixing' not having filed a 90 day report. You haven't filed one in time. If you need anything from an immigration office, and they check to see if you filed a 90 day report, they may well fine you ฿2000 because you didn't.
That's it. That's the only thing that happens. If you don't ever need anything from an immigration office before you leave the country, nothing happens.
On your next entry, count 89 days after you arrive and file a 90 day report in person. You can do that 14 days before or 7 days after that date.
Or you can just not, and pay the fine if they ask you to.
Anonymous participant So, you asked about issues leaving the country but what you're actually concerned about is issues entering the country. Well, no one can really answer that for you. If you've already had issues entering the country that is quite likely to continue as you will still be you, and your immigration history is what it is.
Even if you were told on here that you won't have issues, and then you do, it won't really help to stand there and say 'but some fella on Facebook said it would be ok'.