your web server sees all connections coming from CF IP pool, so if your software has any kind of rate limiting or IP-based binding, it will fail easily. You can fix that by forcing apache/nginx to use CF-Connecting-IP header for client IPs instead.
Other reason can be too aggressive minimizing of JS files, if you enabled it (its off by default), braking IPB scripts.
providing any details about error would help, check app logs too.