I was afraid you'd say that (permalink structure).
I did try removing the index.php, and sure enough, it worked. 
It's weird why this has suddenly stopped working though. Before I upgraded, the forum index worked even w/the index.php. So, not sure what would've changed.
On using index.php: My dilemma is from a SEO perspective. The reason I kept the index.php in my URL is because I was told that changing the permalinks of my blog will result to some kind of search engine penalty. The permalink structure I'm using has been around for the last 3-4 years. And, I have content that might suffer in terms of search engine traffic to start with.
Not to mention, the backlinks and the nightmare of having to fix several internal links. 
So now, I will have to make the decision of whether it's worth risking all the repercussions of changing permalinks, just for Simple:Forum.
I will investigate. But, if it's not worth it, I might have to scrap the idea of using this forum plugin.
A real shame if I have to, because I am enjoying using this plugin.
In any case, thank you very much for taking the time to have a look & offer your suggestions. Really appreciated!