Yes, be sure you check your own morality level. Stats, society I think is how you see your morality level.
For example you always start out at 50 or neutral. Whenever one of the events pops up you pick the bottom one. This would give you evil morality points putting you below 50. Now if you happen to meet the Altarians, they will begin to not like you. They are always Pure good and will not have good relations with any race with less then 50, in fact they will only be friendly once you are at the "Good" morality levels normally.
Choosing evil choices is fine at first but if you want to play as a good player you will need to pick all good choices (top one) to get back to the good level.
Hope to see you at NeoTech http://www.neotechgaming.com/portal.php?sid=2ecd9994d30f785aa7e8d22559148d68 a Starbase for Galciv fans - plus a lot more