Multiple Entry within 90 days...

There's no limit to leave and return within reason period.  The only limit is when leave at 80+ days and trying get another 90 days.  But no problem doing what you're suggesting.

The 90 consecutive days is the maximum time you can stay in Malaysia in any one period. It is not a "count down system".

The restriction is you need to be outside Malaysia for 3 days when you leave. It is 7 days if you leave between 80-90th days.

If you leave, when you re-enter you start theoretically another 90 days of being able to remain legally in Malaysia.

But as Iskandarhack remarks, you may encounter issues at immigration with frequent re-entries. 

Be aware also that the current rule is only 2 overland entries into Thailand from Malaysia per year (no restriction by air).

I didn't know about the overland restriction to/from Thailand. Thanks for information.

To be perfectly accurate it is 2 "visa free" entries within one caledar year Jan-Dec. So subsequent entries would need an application for a multiple entry visa.

Thank you both for the replies.  This is very helpful!

I am a UK citizen and did this a couple of times overnighting in Singaporeor or Thailand no problem, I have now got a visa. A lot of people do it especially if you are not working, . If you are going to stay maybe a year and not work then probably will be fine. However there is never a guarentee.