Business visa, border runs, no work permit. Is it okay?

Hi!
I've been working in Vietnam for a small local company for more than a year now. Initially, I came here for 3 months business visa and the company that I've been working with have helped me extend my visa or get a new invitation letter to do the Border Run every now and then.
Until now what was happening was, after my visa expired after the first three months, the company representative took my passport to the Immigration Department, extended my visa for the next three months and informed that I wouldn't be able to extend the visa the next time and I will have to get a new visa by leaving the country.
Time went by, I got the Invitation letter for the next 3 months, went to MocBai to the 1st border run, got a new 3 months visa. 3 months later, the representative took my passport to the immigration department and extended the visa for the next three months again.
The same thing happened after that, I got the invitation letter, did my 2nd border run and got a new visa. Now, three months later, when it was time for the visa extension, the company representative went to the Immigration Department but came back saying they weren't able to extend the visa for 3 months anymore and they just got the extension for next 1 month. The reason for this simply was that I had done a lot of previous extensions and this time they won't it anymore so I was asked to get a fresh visa.
So, I guess next month I will be doing the same visa run thing to get another 3 months visa.

My concern here is, am I actually allowed to do this? I went through some blog posts saying a foreigner isn't really allowed to work in Vietnam without a work permit for more than 90 days. Getting a work permit hasn't been much of my concerned because I was getting my visa renewed or extended when the time had arrived and I was making sure I don't overstay.
I plan to stay here for some more time and I don't think my company will go through all the process of getting the work permit for me just for that time being. I am starting to feel uncomfortable about this whole thing.
Does this really matter? Am I allowed to work when I don't have a work permit but still have a legal Busines Visa? Is it alright if I keep doing the Visa runs to get the new visa when required?

Sorry for the long post. I really hope somebody has some answer about whats the right thing to do here.