The main problem has been maintaining the spaghetti code that is common in PHP apps written circa 2003. It's not really that bad, its just that things have moved on, and it would be a nightmare for anyone else to make changes to the system. Actually it is getting to be a nightmare for me, mostly because adding new features requires an increasing number of ugly hacks.
The port has been an on-again, off again. I began using the CodeIgniter framework, but changed to Kohana when they added support for PHP5 and started adding useful features not in the other framework.
One of the main issues though, has been the rate of change in both projects - CodeIgniter has been slow and steady, while there has (possibly) been more innovation in Kohana.
In the case of CodeIgniter, it did not always have what I needed (and they weren't taking patches), while Kohana was changing a lot with each major release.
I am definitely not saying that the approach taken by the writers of these frameworks is wrong. They are both good products. But for me I want to be writing business logic, not worrying about how to get a (not available) feature working, or having to rewrite code to account for internal framework changes. Life's too short...
My frustration with both frameworks has led me to look into Ruby on Rails. The byline on the website pretty much sums up what I wanted to experience in my daily work writing software - "Web development that doesn't hurt".
Alongside this we've also had the guys from AbleTech working here on a couple of projects, and I have been impressed with what they have been able to achieve with the Rails framework.
To get started I am porting another smaller web app to Rails. It is going well, and I'm getting to like the syntax very much.
True to the Rails methodology, I got the basic app running and deployed (via Capistrano) in about 20 minutes. From there it was straight into recoding the logic.
I'll be writing a follow-up post soon about the experience.