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Migrating site - problems with SEF URLs

I am very happy with my FusionLite site, and am currently migrating from an IIS server to a Linux/Apache server. I am hoping to use the SEF-friendly URL function, but it seems to be interfering with some, but not all, of the pages on my site. It will change the links and some of the other color definitions to white.

My original site on IIS sans SEF-friendly is here

My new server version is here <-- as you can see, the bug only affects some of my pages, and I know that one a couple of them it's just due to the extension rather than the template (for instance my "available opportunities" page). I've made some changes to the FusionLite core to better suit my use of the template, so if it's possible I'd rather not copy a fresh version.

LumoMongo replied Can't see the differences.

I have opened both links, and both sites look identical to me
Could you give me links or exact locations of differences so I can have a closer look for you?

girljinbink replied Here a few links

Here's a few links where the CSS classes aren't working properly:
link 1
link 2
link 3
It's very random and appears to only happen on some articles.

LumoMongo replied Error 500

That is weird, I am seeing a error 500 - which is due to SEF URL's I think - but I am not sure, so I have asked Skashi to have a quick look. Have CC'd him into your post and asked him, he should get back to you shortly...

skash replied May be conflicts

This could very well be because of the SEF urls as there may be conflicts in the rewriting of the pages. Just send us a support ticket with super admin details and I will take a closer look at your site.

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