Most tournament organizers nowadays use computer aided software to do pairings for the rounds. Whilst some small events may still use manual pairing, using pairing software will probably help the arbiter to do the pairing faster and more efficient (with less mistake). One thing for sure is that manual pairing usually opens more opportunities for arbiter to fix the pairing whereas using a pairing system may minimize the fixing but it does not lessen nor close the door for manipulation. But, to move from one system to the other does not mean an organizer is looking for loop holes to "control the pairing"
I believe we should look at things objectively and always think that there is "another side to the story". If we see someone with a gun, do we assume that he is about to kill someone, or is it because he wants to defend someone? Are we destructive (that it would destroy/cause harm/kill) or constructive (that it would build/develop/save)?
Changing from Swiss Manager to Swiss Perfect could simply happen because of economical reason. Swiss Perfect cost USD49 to purchase whereas Swiss Manager has a price tag of Euro199 (for the full version) and Euro99 (for the light version). In any event, Swiss Manager is much more expensive to own. On top of that, Swiss Perfect has a 30 days free trial period so, using it for small Non-Rated events is very practical. Unless there is an extensive use for FIDE Rated events, then it would be feasible to purchase the Swiss Manager but if not, why waste the extra money unless there is extra money to spend.
Looking at Swiss Manager and Swiss Perfect, one must understand that each system will use different "process" to arrive at a certain pairing. In a tournament where the number of players and their seeding are the same, each system/software may yield a different pairing for each round. But this does not mean the pairings are wrong or the system is flawed. It just means that each is using a different process and logical order but the most important thing is that the processes are "consistent" within each program. If Swiss Manager uses the same "process" to determine the pairing in Round 1, it will use the same logic for Round 7, 11 or 17, and so on. The pairing is only wrong if an event started off with a Swiss Manager system but ends using a Swiss Perfect system (or somewhere in the middle, another different system is being used) i.e. the system used was not consistent. Interesting to note that there is at least 2 popular Swiss Pairing process being used i.e. one which takes color (black and white) into account and the other which does not take colors into account when doing the pairing.
But, it needs to be understood that system is used as a "tool" to aid the Arbiter in doing the Pairing and if the system produced glaring mistake or unjustified pairing, then the Arbiter has the right to overrule and correct the pairing. For all purposes, systems are not 100% perfect so when an irregular situation arises, the Arbiter has the right to change the pairing and this is where his/her pairing methodology needs to follow the correct logical sequence. An Arbiter who have experienced many events will probably be able to identify when a such situation occurs and what needs to be done. If the system (using its internal logic) causes a player to be paired glaringly unfavorable, then the arbiter must correct the situation.
But to learn using the Swiss Manager without learning how to do the pairing manually is very dangerous and illogical - as the saying goes "a little knowledge is very dangerous". Most people who does not understand how to do the pairing will usually take the easy way to just "blame" the system for not doing the pairing correctly. If a person had learned how to do the manual pairing, then it is very easy to check whether the system has made the correct pairing or otherwise. Its like using a calculator but not knowing how to do the calculation manually - "That's the numbers given by the calculator but I don't know how it got those numbers". Same like - "That's the pairing given by the system but I don't know why its like that".
So, before blaming that it is a fixed pairing, get some pairing cards and check the pairing manually. It is a good knowledge to learn hence a player, parents, organizer, coach, etc. can check and "feel" if the system is doing its job correctly instead of taking the easy way of "blaming it on the arbiter for fixing the pairing". But maybe, to certain people , ignorance is bliss therefore, it is easier to blame than to learn. On the same note, it is also sad to have sign up, organize or enroll in such a learning session but not learning anything out of it - and continue to be ignorant
But do take note that even after some sanity checking, the pairing may still feel incorrect. However, one must understand that there are certain exact elements of calculation where the pairing software can calculate much deeper compared to a human brain which may cause the "checking" to be inconclusive. The best way to gauge is to see if the pairing differs very much from the actual pairing or about the same and if it is about the same, or a logical explanation can be found, then it can be concluded that the pairing is correct.
When I did the Blitz Event in Cititel (and some of my smaller events in DATCC), I actually use a projector to perform the pairing sequence using Swiss Manager for people to see. If this method can eliminate the "thought that a pairing is being fixed" then maybe, this method can be use to perform the pairing but..... it may create other issues i.e. the arbiter may not be able to correct a glaring mistake because technically, the pairing has been "published".
In any case, I would like to think that Arbiters are doing their best to perform his/her job and trusting that the he/she will not manipulate the pairing to favor certain players. Why must I think that people are bad?