Issues with reserves team in the main league structure

[nasaiain]

Im looking for a little help. I'm currently working on the swiss leagues, which turn out to be a fairly simple task due to their FA website being the best i've ever come across but i'm having a few problems as you move to the lower leagues.

Basically the swiss league has a national structure down to level 4, from there on 2.Liga and downwards the country is split into 13 regions each with their own league structure down to 5.liga, with no relegation below this

The problem within this structure is that clubs have multiple teams, in some cases up to 5, so obvioulsy i've had to make changes to limit this to a maximum of 3 for each club. The problem i'm having is that when testing the game some of these reserve teams get chucked out of the league at the end of the season.

As an example, TeamX 1st team play in 3.Liga, 2nd team in 4.Liga and the 3rd team 5.Liga. So if the first team get relegated the 2nd team gets forcible relegated, as should be the way, but due to there being the 3rd team in the league they should be relegated to, and knowhere for the 3rd team to go to, the 2nd team just simply get kicked out of the league structure, and replaced the following season by a team from the top division. (usually Basel, who end up playing in 5 divisons with 4 games a week all season).

Also in some cases where the 2nd team can't get promoted due to the first team being in the league above the game is not selecting the next team down the league, it randomly chucks in a top league side, once again usually Basel, into the playoff.

In the past i have made a fantasy league including 1st and 2nd teams, and when the 1st team gets relegated to the lowest division with the 2nd team, they quite happily coexist in the same league. I can't understand why this isn't the case this time around, could it be down to the inclusion of the 3rd teams as well as the 2nd?

Another possible cause could be the way in which i've set up the leagues. Within the 3.Liga each of the 13 regions has a varying number of groups from 2 to 10, so rather than have almost 70 groups in the 3.Liga i've just put in 13 'leagues' with their type modified to group. So for the AFV region rather than having 5 leagues of 11 teams, i've got one of 55 split into 5 groups. Could this have any effect?

By the way this is all done on teh standard editor, i am getting to grips with the advanced editor, but this seemed possible with out using it.