With Indonesia's President Susilo Bambang Yudhoyono in Malaysia for a fence-mending visit with Prime Minister Najib Abdul Razak, the BBC's Jakarta correspondent Karishma Vaswani looks at what has soured relations between the two countries in the first place.
Steps apart - the Indonesian and Malaysian leaders in Kuala Lumpur
It was a Malaysian tourism advert on television, broadcast around the world, that prompted the latest outburst of anger in Indonesia.
The Discovery Channel advert contained a clip of a traditional Indonesian dance, the Balinese pendet dance, and Indonesians felt that Malaysians had stolen their culture - an allegation that is often levelled at the country by its neighbour.
Discovery - the makers of the commercial - apologised. But the episode highlighted the tempestuous relationship that exists between Malaysia and Indonesia on a range of issues - from territorial disputes to problems with migrant workers.
It wasn't always like this. There was a time when some in Indonesia and Malaysia floated the idea of a pan-Malayan region, a powerful geographical entity that would span the two countries, encompassing both populations.
After all, the two nations have so many things in common. They share a history, a similar language, the same religion - even similar food.
So what changed?
Most analysts say the trouble began in the 1960s, soon after both nations won their independence from colonial powers.
'Waiting to strike'
At the time Indonesia and Malaysia almost went to war over disputed claims to the island of Borneo. Indonesia launched the "konfrontasi" movement against Malaysia - and protesters shouted out cries of "ganyang Malaysia" or "crush Malaysia" on the streets of Jakarta.
The leader of Bendera - anti-Malaysia demonstrators in Indonesia
Decades later, those cries were heard again - but this time, not over a territorial dispute - but a cultural one.
Protesters burned the Malaysian flag outside the Malaysian embassy, and again those same words "ganyang Malaysia" were chanted. There were nasty moments when demonstrators stopped people in the streets trying to root out any Malaysians.
The demonstrators call themselves Bendera, or the People's Defence of Democracy. They may only be a small group, but they talk of wanting to wage war against Malaysia.
Their leader, Mustar Bonaventura, says there are at last 600 Indonesians already hiding in Malaysia, waiting to strike.
"Our people are already in Malaysia with the goal of declaring war on them," he told me.
"No one has the guts to do this, only the Bendera Group dares to do this. We need to consider this idea now and we need to consider it seriously - it's obvious that peaceful attempts to resolve our mutual problems haven't worked."
Clashes over culture
The Bendera Group's calls for war have not been taken seriously enough by the Indonesian government to warrant any arrests - but they did say they would monitor the organisation.
What the Indonesian government did take seriously was what they saw as Malaysia's attempts to once again enter the disputed Ambalat area off the island of Borneo earlier this year.
Hanim and other Malays in Jakarta face a difficult time
Both sides have laid claim to this oil-rich region for decades and many said the Indonesians came within moments of firing on a Malaysian vessel that had entered its waters.
The clashes over culture and territory has made life for the 4,000 or so Malaysians living in Indonesia challenging to say the least. Most of them are professionals, sent here by their companies.
I met with some of them at a breakfast meeting of the Malaysian expat club in Jakarta, where I found they were concerned about the situation.
Hanim Hamzah, the club's vice-president, is a Malaysian lawyer who has lived in Jakarta for the last four years. She says she has never seen relations so tense.
"At a meeting with Indonesian clients they asked me where I was from. I hesitated for a moment and thought about what to say. When I finally said I was from Malaysia they went on and on about the whole Malaysia Indonesia issue and told me to be careful."
While circumstances for Malaysians in Indonesia may have changed for the worse since these clashes began, the lives of Indonesian workers in Malaysia have not improved at all.
It is estimated there are about two million Indonesian workers in Malaysia, employed as drivers, maids and construction workers.
There have been horrific reports of cases of abused Indonesian maids in Malaysia which have also heightened tensions between the two nations.
Domestic worker Shirley ran away from her Malaysian employer
Shirley Nia is a domestic servant who has recently returned from Malaysia.
She worked in Kuala Lumpur for a Malaysian employer for just a month - running away after that short time because she was scared she'd be blamed when her boss's dog ran off.
"My boss said her dog is more expensive than me, it's worth more than me," she explained.
"She told me not to lose the dog, but one day the dog ran away, so I ran away. I was afraid. My boss said she would return me to the agents if that ever happened. I've seen some friends tortured by the agents. "
Shirley's story is not an isolated one. In June, the Indonesian government, in response to so many stories of Indonesian domestic servants being abused in Malaysia, enforced a temporary ban on sending domestic workers there.
The hope is that during Indonesian President Susilo Bambang Yudhoyono's visit to Malaysia, the two governments will be able to iron out their differences.
But with so many sensitive problems between them that is likely to be a challenging task.