Are you sure this is what is happening?
Version 7.0.0. When bad code isn't run, good code gives this:
sage: f.q_eigenform(10,'alpha')[3]
(-1/8*zeta4 - 1/4)*alpha^7 + (3/8*zeta4 + 1/8)*alpha^5 + (-1/4*zeta4 + 1)*alpha^3 + (-zeta4 - 1)*alpha
When bad code is run first, good code gives this:
sage: f.q_eigenform(10,'alpha')[3]
(2940134632232014408766657/19352042383840927420034024*zeta4 - 2565054267989270372493119/19352042383840927420034024)*alpha^7 + (-1869921197843988328685619/9676021191920463710017012*zeta4 - 1590788291043697551073545/4838010595960231855008506)*alpha^6 + (-487218429010828867191579/744309322455420285385924*zeta4 - 55395905851779626534807/372154661227710142692962)*alpha^5 + (-505556560719679641283131/744309322455420285385924*zeta4 + 395740922589971800357659/744309322455420285385924)*alpha^4 + (3091086773658381828546971/9676021191920463710017012*zeta4 + 22169159574776632616577397/9676021191920463710017012)*alpha^3 + (6474331895422395046208340/2419005297980115927504253*zeta4 - 2149434331277811094538751/4838010595960231855008506)*alpha^2 + (6666435583064028847954867/4838010595960231855008506*zeta4 - 12722634445968563495188259/4838010595960231855008506)*alpha - 940957015960155394979262/2419005297980115927504253*zeta4 - 3747940737545550772744377/2419005297980115927504253
I am not saying that these are definitely not Galois conjugate. But I am saying that I kind of suspect that these are not Galois conjugate. No! Wait! I am saying they're not Galois conjugate, because
elt=f.q_eigenform(10,'alpha')[3]
gives
x^8 + 16*zeta4*x^6 - 72*x^4 - 64*zeta4*x^2 + 4
if the bad code hasn't run yet, and
x^8 + (7998749126707393770675990/2419005297980115927504253*zeta4 - 47381022823029338213469198/2419005297980115927504253)*x^7 + (88328222560611710210573725/2419005297980115927504253*zeta4 + 402745578098164737879842397/2419005297980115927504253)*x^6 + (-1851973029418246178060665656/2419005297980115927504253*zeta4 - 972520883967381161087609244/2419005297980115927504253)*x^5 + (7012307362677246370736050995/2419005297980115927504253*zeta4 - 4497820941388198664887224012/2419005297980115927504253)*x^4 + (20664072505712818488383157852/2419005297980115927504253*zeta4 + 22847825216496581679001616316/2419005297980115927504253)*x^3 + (-2819149604897477732352436978/186077330613855071346481*zeta4 + 5847356735083004488400198448/186077330613855071346481)*x^2 + (-123986553349389596472324440088/2419005297980115927504253*zeta4 - 22346113370356065142956464904/2419005297980115927504253)*x - 769782031701554576146090878/2419005297980115927504253*zeta4 - 72076427755982334621542375888/2419005297980115927504253
if the bad code has run. We can even coerce elt into elt.parent().absolute_field('b') and then compute the min poly; if the bad code hasn't run the output is sane and if the bad code has run the output is not in Z[x]; thus it seems to me that if I've understood things correctly sage is saying that the coefficient of q^3 of this eigenform is not an algebraic integer, once the bad code has run. More precisely the LCM of the denominators occurring in the coefficients of the min poly once the bad code has run is
13 * 241 * 3541 * 2581177 * 84475877413
So here's a shorter working example of a problem.
First fire up sage 7.0.0 and then cut and paste the below bad code.
And then ignore all that (it has somehow corrupted something??) and do this:
D=ModularSymbols(chi,2,-1).cuspidal_subspace().new_subspace().decomposition();
elt=f.q_eigenform(10,'alpha')[3];
and observe that we get "false". In fact none of the q-expansion coefficients are algebraic integers from q^2 to q^10.
Kevin